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NAMD Papers and Citations

A list of papers citing NAMD is included below.

How to Cite NAMD

The NAMD License Agreement specifies that any reports or published results obtained with NAMD shall acknowledge its use and credit the developers as:

"NAMD was developed by the Theoretical and Computational Biophysics Group in the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign."

Any published work which utilizes NAMD shall include the following reference:

James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone, Joao V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin, Jerome Henin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo, Brian K. Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoit Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kale, Klaus Schulten, Christophe Chipot, and Emad Tajkhorshid.
Scalable molecular dynamics on CPU and GPU architectures with NAMD.
Journal of Chemical Physics, 153:044130, 2020. doi:10.1063/5.0014475
abstract, DOI

Electronic documents shall include a direct link to the official NAMD page:

http://www.ks.uiuc.edu/Research/namd/

Proper citation is essential to continued NIH funding for NAMD development, as it is a primary way in which we demonstrate the value of our software to the scientific community. Thank you for your attention to these details.

Papers About NAMD

James C. Phillips, David J. Hardy, Julio D. C. Maia, John E. Stone, Joao V. Ribeiro, Rafael C. Bernardi, Ronak Buch, Giacomo Fiorin, Jerome Henin, Wei Jiang, Ryan McGreevy, Marcelo C. R. Melo, Brian K. Radak, Robert D. Skeel, Abhishek Singharoy, Yi Wang, Benoit Roux, Aleksei Aksimentiev, Zaida Luthey-Schulten, Laxmikant V. Kale, Klaus Schulten, Christophe Chipot, and Emad Tajkhorshid.
Scalable molecular dynamics on CPU and GPU architectures with NAMD.
Journal of Chemical Physics, 153:044130, 2020. doi:10.1063/5.0014475
DOI

B. Acun, D. J. Hardy, L. V. Kale, K. Li, J. C. Phillips, and J. E. Stone.
Scalable Molecular Dynamics with NAMD on the Summit System.
IBM Journal of Research and Development, 2018.
journal, DOI

James C. Phillips.
What You Should Know About NAMD and Charm++ But Were Hoping to Ignore.
In Proceedings of the Practice and Experience on Advanced Research Computing (PEARC '18). ACM, New York, NY, USA, Article 55, 6 pages. 2018.
DOI

Marcelo C R Melo, Rafael C Bernardi, Till Rudack, Maximilian Scheurer, Christoph Riplinger, James C Phillips, Julio D C Maia, Gerd B Rocha, João V Ribeiro, John E Stone, Frank Neese, Klaus Schulten, & Zaida Luthey-Schulten.
NAMD goes quantum: an integrative suite for hybrid simulations.
Nature Methods, volume 15, pages 351-354, 2018.
DOI

Bilge Acun, Ronak Buch, Laxmikant Kale, and James C. Phillips.
NAMD: Scalable Molecular Dynamics Based on the Charm++ Parallel Runtime System.
Exascale Scientific Applications: Scalability and Performance Portability, Tjerk P. Straatsma, Katerina B. Antypas, and Timothy J. Williams, editors, CRC Press, 2017.
abstract

Brian K. Radak, Christophe Chipot, Donghyuk Suh, Sunhwan Jo, Wei Jiang, James C. Phillips, Klaus Schulten, and Benoît Roux.
Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.
J. Chem. Theory Comput., 2017.
abstract

Joao V. Ribeiro, Rafael C. Bernardi, Till Rudack, John E. Stone, James C. Phillips, Peter L. Freddolino, and Klaus Schulten.
QwikMD-integrative molecular dynamics toolkit for novices and experts.
Scientific Reports, 6:26536, 2016.
abstract

John E. Stone, Antti-Pekka Hynninen, James C. Phillips, and Klaus Schulten.
Early experiences porting the NAMD and VMD molecular simulation and analysis software to GPU-accelerated OpenPOWER platforms.
International Workshop on OpenPOWER for HPC (IWOPH'16), 2016. In Press.
abstract

David J. Hardy, Zhe Wu, James C. Phillips, John E. Stone, Robert D. Skeel, and Klaus Schulten.
Multilevel Summation Method for Electrostatic Force Evaluation.
Journal of Chemical Theory and Computation, 2014. In Press.
abstract, journal

Jeffrey Comer, James Phillips, Klaus Schulten, and Christophe Chipot.
Multiple-replica strategies for free-energy calculations in NAMD: Multiple-walker adaptive biasing force and walker selection rules.
Journal of Chemical Theory and Computation, 2014. In Press.
abstract, journal

James C. Phillips, Yanhua Sun, Nikhil Jain, Eric J. Bohm, and Laximant V. Kale.
Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation.
In Proceedings of the 2014 International Conference for High Performance Computing, Networking, Storage, and Analysis (SC14), 2014.
abstract, conference, journal, benchmark inputs: directory, 2.5K .tar.gz,

James C. Phillips, John E. Stone, Kirby L. Vandivort, Timothy G. Armstrong, Justin M. Wozniak, Michael Wilde, and Klaus Schulten.
Petascale Tcl with NAMD, VMD, and Swift/T.
In SC'14 workshop on High Performance Technical Computing in Dynamic Languages, SC '14. IEEE Press, 2014.
abstract, journal

Wei Jiang, James Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James Gumbart, Yun Luo, Klaus Schulten, and Benoit Roux.
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD.
Computer Physics Communications, 185:908-916, 2014.
abstract, journal

Yanhua Sun, Gengbin Zheng, Chao Mei, Eric J. Bohm, Terry Jones, Laxmikant V. Kale, and James C. Phillips.
Optimizing Fine-grained Communication in a Biomolecular Simulation Application on Cray XK6.
In Proceedings of the 2012 ACM/IEEE Conference on Supercomputing (SC12), 2012.
abstract, conference, journal

David E. Tanner, James C. Phillips, and Klaus Schulten.
GPU/CPU algorithm for generalized Born / solvent-accessible surface area implicit solvent calculations.
Journal of Chemical Theory and Computation, 8:2521-2530, 2012.
abstract, journal

David E. Tanner, Kwok-Yan Chan, James Phillips, and Klaus Schulten.
Parallel generalized Born implicit solvent calculations with NAMD.
Journal of Chemical Theory and Computation, 7:3635-3642, 2011.
abstract, journal

Chao Mei, Yanhua Sun, Gengbin Zheng, Eric J. Bohm, Laxmikant V. Kale, James C. Phillips, and Chris Harrison.
Enabling and Scaling Biomolecular Simulations of 100 Million Atoms on Petascale Machines with a Multicore-optimized Message-driven Runtime.
In Proceedings of the 2011 ACM/IEEE Conference on Supercomputing (SC11), 2011.
abstract, conference, journal

Wei Jiang, David J. Hardy, James C. Phillips, Alexander D. MacKerell, Jr., Klaus Schulten, and Benoit Roux.
High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD.
J. Phys. Chem. Lett., Vol. 2, pp. 87-92, 2011.
abstract, journal

Abhinav Bhatele, Laxmikant V. Kale and Sameer Kumar.
Dynamic Topology Aware Load Balancing Algorithms for Molecular Dynamics Applications.
In Proceedings of 23rd ACM International Conference on Supercomputing (ICS), 2009.
abstract

James C. Phillips, John E. Stone, and Klaus Schulten.
Adapting a message-driven parallel application to GPU-accelerated clusters.
In Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis (SC08), 2008.
abstract, conference

Abhinav Bhatele, Sameer Kumar, Chao Mei, James C. Phillips, Gengbin Zheng, Laxmikant V. Kale.
Overcoming Scaling Challenges in Biomolecular Simulations across Multiple Platforms.
In Proceedings of IEEE International Parallel and Distributed Processing Symposium 2008.
abstract

John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten.
Accelerating molecular modeling applications with graphics processors.
Journal of Computational Chemistry, 28:2618-2640, 2007.
abstract, journal

Klaus Schulten, James C. Phillips, Laxmikant V. Kale, Abhinav Bhatele.
Biomolecular modeling in the era of petascale computing.
In Petascale Computing: Algorithms and Applications, pp. 165-181, D. Bader, Ed., Chapman & Hall / CRC Press, New York, 2008.
abstract

Sameer Kumar, Chao Huang, Gengbin Zheng, Eric Bohm, Abhinav Bhatele, James C. Phillips, Hao Yu, and Laxmikant V. Kale.
Scalable Molecular Dynamics with NAMD on Blue Gene/L.
IBM Journal of Research and Development, Volume 52, No. 1/2, 2007.
abstract

K.Y. Sanbonmatsu and C.-S. Tung.
High performance computing in biology: Multimillion atom simulations of nanoscale systems.
Journal of Structural Biology, 157:470-480, 2007.
journal

Michelle Gower, Jordi Cohen, James Phillips, Richard Kufrin, and Klaus Schulten.
Managing biomolecular simulations in a grid environment with NAMD-G.
Proceedings of the 2006 TeraGrid Conference, 2006. In Press.
abstract

Sameer Kumar, Chao Huang, Gheorghe Almasi, and Laxmikant V. Kale.
Achieving Strong Scaling with NAMD on Blue Gene/L.
Proceedings of IEEE International Parallel & Distributed Processing Symposium 2006, 2006.
abstract

Laxmikant V. Kale, Klaus Schulten, Robert D. Skeel, Glenn Martyna, Mark Tuckerman, James C. Phillips, Sameer Kumar, and Gengbin Zheng.
Biomolecular modeling using parallel supercomputers.
In S. Aluru, editor, Handbook of computational molecular biology, pp. 34.1-34.43. Taylor and Francis, 2005.
abstract

James C. Phillips, Rosemary Braun, Wei Wang, James Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant Kale, and Klaus Schulten.
Scalable molecular dynamics with NAMD.
Journal of Computational Chemistry, 26:1781-1802, 2005. abstract, journal

Joachim Hein, Fiona Reid, Lorna Smith, Ian Bush, Martyn Guest, and Paul Sherwood.
On the performance of molecular dynamics applications on current high-end systems.
Phil. Trans. R. Soc. A, 363:1987-1998, 2005.
journal

James C. Phillips, Gengbin Zheng, Sameer Kumar, and Laxmikant V. Kal�.
NAMD: Biomolecular Simulation on Thousands of Processors.
Proceedings of the IEEE/ACM SC2002 Conference. IEEE Press, 2002. Technical Paper 277.
abstract, pdf

Robert K. Brunner, James C. Phillips, Laxmikant V. Kal�.
Scalable Molecular Dynamics for Large Biomolecular Systems.
Proceedings of the IEEE/ACM SC2000 Conference. IEEE Press, 2000. Technical Paper 271.
abstract, pdf

R. Sharma, M. Zeller, V. I. Pavlovic, T. S. Huang, Z. Lo, S. Chu, Y. Zhao, J. Phillips, and K. Schulten.
Speech/Gesture Interface to a Visual Computing Environment.
IEEE Computer Graphics and Applications, March/April 2000, 29-37.
abstract,

Laxmikant Kal�, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten.
NAMD2: Greater scalability for parallel molecular dynamics.
Journal of Computational Physics, 151:283-312, 1999.
abstract

Robert Brunner, Laxmikant Kal�, and James Phillips.
Flexibility and Inter-operability in a Parallel Biomolecular Dynamics Code.
In M.E. Henderson, C.R. Anderson, and S.L. Lyons, editors, Object Oriented Methods for Interoperable Scientific and Engineering Computing, Proceedings in Applied Mathematics 99, 1999.

James C. Phillips, Robert Brunner, Aritomo Shinozaki, Milind Bhandarkar, Neal Krawetz, Laxmikant Kal�, Robert D. Skeel, and Klaus Schulten.
Avoiding algorithmic obfuscation in a message-driven parallel MD code.
In P. Deuflhard, J. Hermans, B. Leimkuhler, A.E. Mark, S. Reich, and R.D. Skeel, editors, Computational Molecular Dynamics: Challenges, Methods, Ideas, Lecture Notes in Computational Science and Engineering, 4:472-482, 1999. Springer-Verlag.
abstract

L. V. Kal�, M. Bhandarkar, R. Brunner, N. Krawetz, J. Phillips, and A. Shinozaki.
NAMD: A Case Study in Multilingual Parallel Programming.
In Z. Li, P.-C. Yew, S. Chatterjee, C.-H. Huang, P. Sadayappan, and D. Sehr, editors, Languages and Compilers for Parallel Computing, Lecture Notes in Computer Science, 1366:367-381, 1998. Springer-Verlag.
abstract

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kal�, Robert D. Skeel, and Klaus Schulten.
NAMD-A parallel, object-oriented molecular dynamics program.
International Journal of Supercomputer Applications and High Performance Computing, 10:251-268, 1996.
abstract

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kal�, Robert Skeel, Klaus Schulten, and Richard Kufrin.
MDScope-A visual computing environment for structural biology.
Computational Physics Communications, 91:111-134, 1995.
abstract

Mark Nelson, William Humphrey, Attila Gursoy, Andrew Dalke, Laxmikant Kal�, Robert Skeel, Klaus Schulten, and Richard Kufrin.
MDScope-A visual computing environment for structural biology.
In S.N. Atluri, G. Yagawa, and T.A. Cruse, editors, Computational Mechanics 95, volume 1, pages 476-481, 1995.
abstract

Papers Citing NAMD

The "full text" links lead to Google Scholar searches for the article. We do not provide copies of these articles ourselves. Articles by TCBG members are available in the TCBG Publications Database.

7066 citations found April 29, 2016.

Shen, Meng; Keten, Sinan; Lueptow, Richard M.
Rejection mechanisms for contaminants in polyamide reverse osmosis membranes
JOURNAL OF MEMBRANE SCIENCE, 509:36-47, JUL 1 2016
abstract, full text, DOI:10.1016/j.memsci.2016.02.043

Chiang, Ying-Chih; Wang, Yi
Virtual Substitution Scan Via Single-Step Free Energy Perturbation
BIOPOLYMERS, 105:324-336, JUN 2016
abstract, full text, DOI:10.1002/bip.22820

Shen, Meng; Keten, Sinan; Lueptow, Richard M.
Dynamics of water and solute transport in polymeric reverse osmosis membranes via molecular dynamics simulations
JOURNAL OF MEMBRANE SCIENCE, 506:95-108, MAY 15 2016
abstract, full text, DOI:10.1016/j.memsci.2016.01.051

Eifler, Jay; Podgornik, Rudi; Steinmetz, Nicole F.; French, Roger H.; Parsegian, V. Adrian; Ching, Wai-Yim
Charge distribution and hydrogen bonding of a collagen (2)-chain in vacuum, hydrated, neutral, and charged structural models
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 116:681-691, MAY 5 2016
abstract, full text, DOI:10.1002/qua.25089

Roussou, Roza-Eleftheria; Karatasos, Kostas
Graphene/poly(ethylene glycol) nanocomposites as studied by molecular dynamics simulations
MATERIALS & DESIGN, 97:163-174, MAY 5 2016
abstract, full text, DOI:10.1016/j.matdes.2016.02.078

Salmas, Ramin Ekhteiari; Senturk, Murat; Yurtsever, Mine; Durdagi, Serdar
Discovering novel carbonic anhydrase type IX (CA IX) inhibitors from seven million compounds using virtual screening and in vitro analysis
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 31:425-433, MAY 3 2016
abstract, full text, DOI:10.3109/14756366.2015.1036049

Somogyi, Endre; Mansour, Andrew Abi; Ortoleva, Peter J.
ProtoMD: A prototyping toolkit for multiscale molecular dynamics
COMPUTER PHYSICS COMMUNICATIONS, 202:337-350, MAY 2016
abstract, full text, DOI:10.1016/j.cpc.2016.01.014

Kopaczynska, M.; Schulz, A.; Fraczkowska, K.; Kraszewski, S.; Podbielska, H.; Fuhrhop, J. H.
Selective condensation of DNA by aminoglycoside antibiotics
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 45:287-299, MAY 2016
abstract, full text, DOI:10.1007/s00249-015-1095-9

Du, Hongbo; Qian, Xianghong
The Hydration Properties of Carboxybetaine Zwitterion Brushes
JOURNAL OF COMPUTATIONAL CHEMISTRY, 37:877-885, APR 15 2016
abstract, full text, DOI:10.1002/jcc.24234

Osman, Roman; Mezei, Mihaly; Engel, Stanislav
The Role of Protein "Stability Patches" in Molecular Recognition: A Case Study of the Human Growth Hormone-Receptor Complex
JOURNAL OF COMPUTATIONAL CHEMISTRY, 37:913-919, APR 15 2016
abstract, full text, DOI:10.1002/jcc.24276

Arthur, Evan J.; Brooks, Charles L., I.I.I.
Parallelization and Improvements of the Generalized Born Model with a Simple sWitching Function for Modern Graphics Processors
JOURNAL OF COMPUTATIONAL CHEMISTRY, 37:927-939, APR 15 2016
abstract, full text, DOI:10.1002/jcc.24280

Kucuk, Sami Emre; Sezer, Deniz
Multiscale computational modeling of C-13 DNP in liquids
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:9353-9357, APR 14 2016
abstract, full text, DOI:10.1039/c6cp01028h

Yang, Jing; Bonomi, Massimiliano; Calero, Carles; Marti, Jordi
Free energy landscapes of sodium ions bound to DMPC-cholesterol membrane surfaces at infinite dilution
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:9036-9041, APR 7 2016
abstract, full text, DOI:10.1039/c5cp05527j

Salveson, Patrick J.; Spencer, Ryan K.; Nowick, James S.
X-ray Crystallographic Structure of Oligomers Formed by a Toxic beta-Hairpin Derived from alpha-Synuclein: Trimers and Higher-Order Oligomers
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 138:4458-4467, APR 6 2016
abstract, full text, DOI:10.1021/jacs.5b13261

Zhou, Wenjin; Rossetto, Allison M.; Pang, Xiaodong; Zhou, Linxiang
Computational full electron structure study of biological activity in Cyclophilin A
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 34:870-876, APR 2 2016
abstract, full text, DOI:10.1080/07391102.2015.1057527

Zhao, Yuan; Chen, Nanhao; Wang, Chaojie; Cao, Zexing
A Comprehensive Understanding of Enzymatic Catalysis by Hydroxynitrile Lyases with S Stereoselectivity from the alpha/beta-Hydrolase Superfamily: Revised Role of the Active-Site Lysine and Kinetic Behavior of Substrate Delivery and Sequential Product Release
ACS CATALYSIS, 6:2145-2157, APR 2016
abstract, full text, DOI:10.1021/acscatal.5b02855

Mendoza, Fernanda; Gomez, Hansel; Lluch, Jose M.; Masgrau, Laura
alpha 1,4-N-Acetylhexosaminyltransferase EXTL2: The Missing Link for Understanding Glycosidic Bond Biosynthesis with Retention of Configuration
ACS CATALYSIS, 6:2577-2589, APR 2016
abstract, full text, DOI:10.1021/acscatal.5b02945

Brown, Patricia M. G. E.; Aurousseau, Mark R. P.; Musgaard, Maria; Biggin, Philip C.; Bowie, Derek
Kainate receptor pore-forming and auxiliary subunits regulate channel block by a novel mechanism
JOURNAL OF PHYSIOLOGY-LONDON, 594:1821-1840, APR 1 2016
abstract, full text, DOI:10.1113/JP271690

Jang, Hyunbum; Banerjee, Avik; Chavan, Tanmay S.; Lu, Shaoyong; Zhang, Jian; Gaponenko, Vadim; Nussinov, Ruth
The higher level of complexity of K-Ras4B activation at the membrane
FASEB JOURNAL, 30:1643-1655, APR 2016
abstract, full text, DOI:10.1096/fj.15-279091

Hui, Wen-Qi; Cheng, Qi; Liu, Tian-Yu; Ouyang, Qin
Homology modeling, docking, and molecular dynamics simulation of the receptor GALR2 and its interactions with galanin and a positive allosteric modulator
JOURNAL OF MOLECULAR MODELING, 22 Art. No. 90, APR 2016
abstract, full text, DOI:10.1007/s00894-016-2944-x

Ilizaliturri-Flores, Ian; Correa-Basurto, Jose; Bello, Martiniano; Rosas-Trigueros, Jorge L.; Zamora-Lopez, Beatriz; Benitez-Cardoza, Claudia G.; Zamorano-Carrillo, Absalom
Mapping the intrinsically disordered properties of the flexible loop domain of Bcl-2: a molecular dynamics simulation study
JOURNAL OF MOLECULAR MODELING, 22 Art. No. 98, APR 2016
abstract, full text, DOI:10.1007/s00894-016-2940-1

Hilbert, Manuel; Noga, Akira; Frey, Daniel; Hamel, Virginie; Guichard, Paul; Kraatz, Sebastian H. W.; Pfreundschuh, Moritz; Hosner, Sarah; Flueckiger, Isabelle; Jaussi, Rolf; Wieser, Mara M.; Thieltges, Katherine M.; Deupi, Xavier; Mueller, Daniel J.; Kammerer, Richard A.; Goenczy, Pierre; Hirono, Masafumi; Steinmetz, Michel O.
SAS-6 engineering reveals interdependence between cartwheel and microtubules in determining centriole architecture
NATURE CELL BIOLOGY, 18:393-+, APR 2016
abstract, full text, DOI:10.1038/ncb3329

Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C.; McCammon, J. Andrew
General trends of dihedral conformational transitions in a globular protein
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84:501-514, APR 2016
abstract, full text, DOI:10.1002/prot.24996

Shim, Joong-Youn; Khurana, Leepakshi; Kendall, Debra A.
Computational analysis of the CB1 carboxyl-terminus in the receptor-G protein complex
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84:532-543, APR 2016
abstract, full text, DOI:10.1002/prot.24999

Liberato, Marcelo V.; Silveira, Rodrigo L.; Prates, Erica T.; de Araujo, Evandro A.; Pellegrini, Vanessa O. A.; Camilo, Cesar M.; Kadowaki, Marco A.; Neto, Mario de O.; Popov, Alexander; Skaf, Munir S.; Polikarpov, Igor
Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism
SCIENTIFIC REPORTS, 6 Art. No. 23473, APR 1 2016
abstract, full text, DOI:10.1038/srep23473

Wang, Qi; Heizer, Esley; Rosa, Bruce A.; Wildman, Scott A.; Janetka, James W.; Mitreva, Makedonka
Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting
INFECTION GENETICS AND EVOLUTION, 39:201-211, APR 2016
abstract, full text, DOI:10.1016/j.meegid.2016.01.025

Chandramouli, Balasubramanian; Di Maio, Danilo; Mancini, Giordano; Brancato, Giuseppe
Introducing an artificial photo-switch into a biological pore: A model study of an engineered alpha-hemolysin
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1858:689-697, APR 2016
abstract, full text, DOI:10.1016/j.bbamem.2015.12.030

Kyriakou, Panagiota K.; Ekblad, Bie; Kristiansen, Per Eugen; Kaznessis, Yiannis N.
Interactions of a class IIb bacteriocin with a model lipid bilayer, investigated through molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1858:824-835, APR 2016
abstract, full text, DOI:10.1016/j.bbamem.2016.01.005

Azamat, Jafar; Khataee, Alireza; Joo, Sang Woo
Molecular dynamics simulations of trihalomethanes removal from water using boron nitride nanosheets
JOURNAL OF MOLECULAR MODELING, 22 Art. No. 82, APR 2016
abstract, full text, DOI:10.1007/s00894-016-2939-7

He, Jianfeng; Wang, Jiabin; Hu, Jun; Sun, Jielin; Czajkowsky, Daniel Mark; Shao, Zhifeng
Single molecule atomic force microscopy of aerolysin pore complexes reveals unexpected star-shaped topography
JOURNAL OF MOLECULAR RECOGNITION, 29:174-181, APR 2016
abstract, full text, DOI:10.1002/jmr.2517

Kaplan, Elise; Guichou, Jean-Francois; Chaloin, Laurent; Kunzelmann, Simone; Leban, Nadia; Serpersu, Engin H.; Lionne, Corinne
Aminoglycoside binding and catalysis specificity of aminoglycoside 2 ''-phosphotransferase IVa: A thermodynamic, structural and kinetic study
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1860:802-813, APR 2016
abstract, full text, DOI:10.1016/j.bbagen.2016.01.016

Devineni, Subba Rao; Golla, Madhava; Chamarthi, Naga Raju; Meriga, Balaji; Saddala, Madhu Sudhana; Asupathri, Usha Rani
2-Amino-2,3-dihydro-1H-2 lambda(5)-[1,3,2]diazaphospholo[4,5-b]pyridin-2-one-based urea and thiourea derivatives: synthesis, molecular docking study and evaluation of anti-inflammatory and antimicrobial activities
MEDICINAL CHEMISTRY RESEARCH, 25:751-768, APR 2016
abstract, full text, DOI:10.1007/s00044-016-1518-x

Caruso, Icaro Putinhon; Barbosa Filho, Jose Maria; de Araujo, Alexandre Suman; de Souza, Fatima Pereira; Fossey, Marcelo Andres; Cornelio, Marinonio Lopes
An integrated approach with experimental and computational tools outlining the cooperative binding between 2-phenylchromone and human serum albumin
FOOD CHEMISTRY, 196:935-942, APR 1 2016
abstract, full text, DOI:10.1016/j.foodchem.2015.10.027

Carballo-Pacheco, Martin; Strodel, Birgit
Advances in the Simulation of Protein Aggregation at the Atomistic Scale
JOURNAL OF PHYSICAL CHEMISTRY B, 120:2991-2999, MAR 31 2016
abstract, full text, DOI:10.1021/acs.jpcb.6b00059

Punihaole, David; Workman, Riley J.; Hong, Zhenmin; Madura, Jeffry D.; Asher, Sanford A.
Polyglutamine Fibrils: New Insights into Antiparallel beta-Sheet Conformational Preference and Side Chain Structure
JOURNAL OF PHYSICAL CHEMISTRY B, 120:3012-3026, MAR 31 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b11380

Saurabh, Suman; Glaser, Matthew A.; Lansac, Yves; Maiti, Prabal K.
Atomistic Simulation of Stacked Nucleosome Core Particles: Tail Bridging, the H4 Tail, and Effect of Hydrophobic Forces
JOURNAL OF PHYSICAL CHEMISTRY B, 120:3048-3060, MAR 31 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b11863

Kannan, Srinivasaraghavan; Lane, David P.; Verma, Chandra S.
Long range recognition and selection in IDPs: the interactions of the C-terminus of p53
SCIENTIFIC REPORTS, 6 Art. No. 23750, MAR 31 2016
abstract, full text, DOI:10.1038/srep23750

Vukovic, Lela; Chipot, Christophe; Makino, Debora L.; Conti, Elena; Schulten, Klaus
Molecular Mechanism of Processive 3 ' to 5 ' RNA Translocation in the Active Subunit of the RNA Exosome Complex
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 138:4069-4078, MAR 30 2016
abstract, full text, TCBG publications, DOI:10.1021/jacs.5b12065

Mukhi, Nitika; Dhindwal, Sonali; Uppal, Sheetal; Kapoor, Abhijeet; Arya, Richa; Kumar, Pravindra; Kaur, Jagreet; Kundu, Suman
Structural and Functional Significance of the N- and C-Terminal Appendages in Arabidopsis Truncated Hemoglobin
BIOCHEMISTRY, 55:1724-1740, MAR 29 2016
abstract, full text, DOI:10.1021/acs.biochem.5b01013

Patel, Dharmeshkumar; Mahdavi, Somayeh; Kuyucak, Serdar
Computational Study of Binding of mu-Conotoxin GIIIA to Bacterial Sodium Channels Na(V)Ab and NaVRh
BIOCHEMISTRY, 55:1929-1938, MAR 29 2016
abstract, full text, DOI:10.1021/acs.biochem.5b01324

Motlagh, Hesam N.; Toptygin, Dmitri; Kaiser, Christian M.; Hilser, Vincent J.
Single-Molecule Chemo-Mechanical Spectroscopy Provides Structural Identity of Folding Intermediates
BIOPHYSICAL JOURNAL, 110:1280-1290, MAR 29 2016
abstract, full text, DOI:10.1016/j.bpj.2015.12.042

Nishima, Wataru; Mizukami, Wataru; Tanaka, Yoshiki; Ishitani, Ryuichiro; Nureki, Osamu; Sugita, Yuji
Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter
BIOPHYSICAL JOURNAL, 110:1346-1354, MAR 29 2016
abstract, full text, DOI:10.1016/j.bpj.2016.01.027

Khan, Hanif M.; He, Tao; Fuglebakk, Edvin; Grauffel, Cedric; Yang, Boqian; Roberts, Mary F.; Gershenson, Anne; Reuter, Nathalie
A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding
BIOPHYSICAL JOURNAL, 110:1367-1378, MAR 29 2016
abstract, full text, DOI:10.1016/j.bpj.2016.02.020

Shams, Hengameh; Golji, Javad; Garakani, Kiavash; Mofrad, Mohammad R. K.
Dynamic Regulation of alpha-Actinin's Calponin Homology Domains on F-Actin
BIOPHYSICAL JOURNAL, 110:1444-1455, MAR 29 2016
abstract, full text, DOI:10.1016/j.bpj.2016.02.024

Wulf, Sarah F.; Ropars, Virginie; Fujita-Becker, Setsuko; Oster, Marco; Hofhaus, Goetz; Trabuco, Leonardo G.; Pylypenko, Olena; Sweeney, H. Lee; Houdusse, Anne M.; Schroeder, Rasmus R.
Force-producing ADP state of myosin bound to actin
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 113:E1844-E1852, MAR 29 2016
abstract, full text, DOI:10.1073/pnas.1516598113

Luan, Binquan; Zhou, Ruhong
Wettability and friction of water on a MoS2 nanosheet
APPLIED PHYSICS LETTERS, 108 Art. No. 131601, MAR 28 2016
abstract, full text, DOI:10.1063/1.4944840

Reese, Anna; List, Nanna Holmgaard; Kongsted, Jacob; Solov'yov, Ilia A.
How Far Does a Receptor Influence Vibrational Properties of an Odorant?
PLOS ONE, 11 Art. No. e0152345, MAR 25 2016
abstract, full text, DOI:10.1371/journal.pone.0152345

Liu, Ying; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
How Does the Solvent Modulate Shuttling in a Pillararene/Imidazolium [2]Rotaxane? Insights from Free Energy Calculations
JOURNAL OF PHYSICAL CHEMISTRY C, 120:6287-6293, MAR 24 2016
abstract, full text, DOI:10.1021/acs.jpcc.6b00852

Chopra, Nikita; Wales, Thomas E.; Joseph, Raji E.; Boyken, Scott E.; Engen, John R.; Jernigan, Robert L.; Andreotti, Amy H.
Dynamic Allostery Mediated by a Conserved Tryptophan in the Tec Family Kinases
PLOS ONE, 11 Art. No. e1004826, MAR 24 2016
abstract, full text, DOI:10.1371/journal.pcbi.1004826

Fuentealba, Matias; Munoz, Rodrigo; Maturana, Pablo; Krapp, Adriana; Cabrera, Ricardo
Determinants of Cofactor Specificity for the Glucose-6-Phosphate Dehydrogenase from Escherichia coli: Simulation, Kinetics and Evolutionary Studies
PLOS ONE, 11 Art. No. e0152403, MAR 24 2016
abstract, full text, DOI:10.1371/journal.pone.0152403

Hardy, David J.; Wolff, Matthew A.; Xia, Jianlin; Schulten, Klaus; Skeel, Robert D.
Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 144 Art. No. 114112, MAR 21 2016
abstract, full text, TCBG publications, DOI:10.1063/1.4943868

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy
Effects of protein-DNA complex formation on the intermolecular vibrational density of states of interfacial water
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:7780-7788, MAR 21 2016
abstract, full text, DOI:10.1039/c5cp07562a

Deng, Qingming; Pan, Jun; Yin, Xiaohui; Wang, Xiaofeng; Zhao, Lina; Kang, Seung-gu; Jimenez-Cruz, Camilo A.; Zhou, Ruhong; Li, Jingyuan
Toward high permeability, selectivity and controllability of water desalination with FePc nanopores
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:8140-8147, MAR 21 2016
abstract, full text, DOI:10.1039/c6cp00322b

Carson, Spencer; Wilson, James; Aksimentiev, Aleksei; Weigele, Peter R.; Wanunu, Meni
Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA
NUCLEIC ACIDS RESEARCH, 44:2085-2092, MAR 18 2016
abstract, full text, DOI:10.1093/nar/gkv1199

Speltz, Thomas E.; Fanning, Sean W.; Mayne, Christopher G.; Fowler, Colin; Tajkhorshid, Emad; Greene, Geoffrey L.; Moore, Terry W.
Stapled Peptides with -Methylated Hydrocarbon Chains for the Estrogen Receptor/Coactivator Interaction
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 55:4252-4255, MAR 18 2016
abstract, full text, DOI:10.1002/anie.201510557

Rossi, Pia; Sterlini, Bruno; Castroflorio, Enrico; Marte, Antonella; Onofri, Franco; Valtorta, Flavia; Maragliano, Luca; Corradi, Anna; Benfenati, Fabio
A Novel Topology of Proline-rich Transmembrane Protein 2 (PRRT2): HINTS FOR AN INTRACELLULAR FUNCTION AT THE SYNAPSE
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:6111-6123, MAR 18 2016
abstract, full text, DOI:10.1074/jbc.M115.683888

Gan, Quan; Dai, Jian; Zhou, Huan-Xiang; Wollmuth, Lonnie P.
The Transmembrane Domain Mediates Tetramerization of -Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:6595-6606, MAR 18 2016
abstract, full text, DOI:10.1074/jbc.M115.686246

Zhang, Yunfeng; Ling, Zhenmin; Du, Guocheng; Chen, Jian; Kang, Zhen
Improved Production of Active Streptomyces griseus Trypsin with a Novel Auto-Catalyzed Strategy
SCIENTIFIC REPORTS, 6 Art. No. 23158, MAR 17 2016
abstract, full text, DOI:10.1038/srep23158

Katava, Marina; Kalimeri, Maria; Stirnemann, Guillaume; Sterpone, Fabio
Stability and Function at High Temperature. What Makes a Thermophilic GTPase Different from Its Mesophilic Homologue
JOURNAL OF PHYSICAL CHEMISTRY B, 120:2721-2730, MAR 17 2016
abstract, full text, DOI:10.1021/acs.jpcb.6b00306

Hosseinzadeh, Parisa; Mirts, Evan N.; Pfister, Thomas D.; Gao, Yi-Gui; Mayne, Christopher; Robinson, Howard; Tajkhorshid, Emad; Lu, Yi
Enhancing Mn(II)-Binding and Manganese Peroxidase Activity in a Designed Cytochrome c Peroxidase through Fine-Tuning Secondary-Sphere Interactions
BIOCHEMISTRY, 55:1494-1502, MAR 15 2016
abstract, full text, DOI:10.1021/acs.biochem.5b01299

Angarica, Vladimir Espinosa; Orozco, Modesto; Sancho, Javier
Exploring the complete mutational space of the LDL receptor LA5 domain using molecular dynamics: linking SNPs with disease phenotypes in familial hypercholesterolemia
HUMAN MOLECULAR GENETICS, 25:1233-1246, MAR 15 2016
abstract, full text, DOI:10.1093/hmg/ddw004

Jones, Peter M.; George, Anthony M.
Computational analysis of the MCoTI-II plant defence knottin reveals a novel intermediate conformation that facilitates trypsin binding
SCIENTIFIC REPORTS, 6 Art. No. 23174, MAR 15 2016
abstract, full text, DOI:10.1038/srep23174

Azamat, Jafar; Khataee, Alireza; Joo, Sang Woo
Separation of copper and mercury as heavy metals from aqueous solution using functionalized boron nitride nanosheets: A theoretical study
JOURNAL OF MOLECULAR STRUCTURE, 1108:144-149, MAR 15 2016
abstract, full text, DOI:10.1016/j.molstruc.2015.11.058

Baul, Upayan; Kanth, J. Maruthi Pradeep; Anishetty, Ramesh; Vemparala, Satyavani
Effect of simple solutes on the long range dipolar correlations in liquid water
JOURNAL OF CHEMICAL PHYSICS, 144 Art. No. 104502, MAR 14 2016
abstract, full text, DOI:10.1063/1.4943097

Luan, Binquan; Huynh, Tien; Zhou, Ruhong
Potential Interference of Protein-Protein Interactions by Graphyne
JOURNAL OF PHYSICAL CHEMISTRY B, 120:2124-2131, MAR 10 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b11449

Zuo, Zhicheng; Weng, Jingwei; Wang, Wenning
Insights into the Inhibitory Mechanism of D13-9001 to the Multidrug Transporter AcrB through Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 120:2145-2154, MAR 10 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b11942

Jiang, Tao; Han, Wei; Maduke, Merritt; Tajkhorshid, Emad
Molecular Basis for Differential Anion Binding and Proton Coupling in the CI-/H+ Exchanger CIC-ec1
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 138:3066-3075, MAR 9 2016
abstract, full text, DOI:10.1021/jacs.5b12062

Prakash, Priyanka; Zhou, Yong; Liang, Hong; Hancock, John F.; Gorfe, Alemayehu A.
Oncogenic K-Ras Binds to an Anionic Membrane in Two Distinct Orientations: A Molecular Dynamics Analysis
BIOPHYSICAL JOURNAL, 110:1125-1138, MAR 8 2016
abstract, full text, DOI:10.1016/j.bpj.2016.01.019

Ben Halima, Saoussen; Mishra, Sabyashachi; Raja, K. Muruga Poopathi; Willem, Michael; Baici, Antonio; Simons, Kai; Bruestle, Oliver; Koch, Philipp; Haass, Christian; Caflisch, Amedeo; Rajendran, Lawrence
Specific Inhibition of beta-Secretase Processing of the Alzheimer Disease Amyloid Precursor Protein
CELL REPORTS, 14:2127-2141, MAR 8 2016
abstract, full text, DOI:10.1016/j.celrep.2016.01.076

Borthwick, Lee A.; Kerbiriou, Mathieu; Taylor, Christopher J.; Cozza, Giorgio; Lascu, Ioan; Postel, Edith H.; Cassidy, Diane; Trouve, Pascal; Mehta, Anil; Robson, Louise; Muimo, Richmond
Role of Interaction and Nucleoside Diphosphate Kinase B in Regulation of the Cystic Fibrosis Transmembrane Conductance Regulator Function by cAMP-Dependent Protein Kinase A
PLOS ONE, 11 Art. No. e0149097, MAR 7 2016
abstract, full text, DOI:10.1371/journal.pone.0149097

Vergadou, Niki; Androulaki, Eleni; Hill, Joerg-Ruediger; Economou, Ioannis G.
Molecular simulations of imidazolium-based tricyanomethanide ionic liquids using an optimized classical force field
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:6850-6860, MAR 7 2016
abstract, full text, DOI:10.1039/c5cp05892a

Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui
Free Energy Simulations with the AMOEBA Polarizable Force Field and Metadynamics on GPU Platform
JOURNAL OF COMPUTATIONAL CHEMISTRY, 37:614-622, MAR 5 2016
abstract, full text, DOI:10.1002/jcc.24227

Takahashi, Tsukasa; Ngo, Bao C. Vo; Xiao, Leyang; Arya, Gaurav; Heller, Michael J.
Molecular mechanical properties of short-sequence peptide enzyme mimics
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 34:463-474, MAR 3 2016
abstract, full text, DOI:10.1080/07391102.2015.1039586

Skelton, A. A.; Khedkar, V. M.; Fried, J. R.
All-atom molecular dynamics simulations of an artificial sodium channel in a lipid bilayer: the effect of water solvation/desolvation of the sodium ion
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 34:529-539, MAR 3 2016
abstract, full text, DOI:10.1080/07391102.2015.1044473

Mogami, George; Suzuki, Makoto; Matubayasi, Nobuyuki
Spatial-Decomposition Analysis of Energetics of Ionic Hydration
JOURNAL OF PHYSICAL CHEMISTRY B, 120:1813-1821, MAR 3 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b09481

Zvereva, Elena E.; Katsyuba, Sergey A.; Dyson, Paul J.; Aleksandrov, Alexey V.
Solvation of Palladium Clusters in an Ionic Liquid: A QM/MM Molecular Dynamics Study
JOURNAL OF PHYSICAL CHEMISTRY C, 120:4596-4604, MAR 3 2016
abstract, full text, DOI:10.1021/acs.jpcc.5b11229

Pietra, Francesco
On the Permeation by Dioxygen of the Cofactor-Independent Unusual Oxygenase RhCC, in Complex with Substrate 4-Hydroxyphenylenolpyruvate. A Molecular Dynamics Investigation
CHEMISTRY & BIODIVERSITY, 13:331-335, MAR 2016
abstract, full text, DOI:10.1002/cbdv.201500211

Setiadi, Jeffry; Kuyucak, Serdar
Computational Investigation of the Effect of Lipid Membranes on Ion Permeation in Gramicidin A
MEMBRANES, 6, MAR 2016
abstract, full text, DOI:10.3390/membranes6010020

Kidmose, Rune T.; Andersen, Gregers R.
Interacting with the Human Insulin Receptor
STRUCTURE, 24:351-352, MAR 1 2016
abstract, full text, DOI:10.1016/j.str.2016.02.003

Croll, Tristan I.; Smith, Brian J.; Margetts, Mai B.; Whittaker, Jonathan; Weiss, Michael A.; Ward, Colin W.; Lawrence, Michael C.
Higher-Resolution Structure of the Human Insulin Receptor Ectodomain: Multi-Modal Inclusion of the Insert Domain
STRUCTURE, 24:469-476, MAR 1 2016
abstract, full text, DOI:10.1016/j.str.2015.12.014

Lucius, Melissa; Falatach, Rebecca; McGlone, Cameron; Makaroff, Katherine; Danielson, Alex; Williams, Cameron; Nix, Jay C.; Konkolewicz, Dominik; Page, Richard C.; Berberich, Jason A.
Investigating the Impact of Polymer Functional Groups on the Stability and Activity of Lysozyme-Polymer Conjugates
BIOMACROMOLECULES, 17:1123-1134, MAR 2016
abstract, full text, DOI:10.1021/acs.biomac.5b01743

Li Qing; Yang Deng-Feng; Wang Jian-Hua; Wu Qi; Liu Qing-Zhi
Biomimetic Modification and Desalination Behavior of (15,15) Carbon Nanotubes with a Diameter Larger than 2 nm
ACTA PHYSICO-CHIMICA SINICA, 32:691-700, MAR 2016
abstract, full text, DOI:10.3866/PKU.WHXB201512182

Elmore, Donald E.
Why should biochemistry students be introduced to molecular dynamics simulationsand how can we introduce them?
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 44:118-123, MAR-APR 2016
abstract, full text, DOI:10.1002/bmb.20943

Lundquist, Karl; Herndon, Conner; Harty, Tyson H.; Gumbart, James C.
Accelerating the use of molecular modeling in the high school classroom with VMD Lite
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 44:124-129, MAR-APR 2016
abstract, full text, DOI:10.1002/bmb.20940

Spitznagel, Benjamin; Pritchett, Paige R.; Messina, Troy C.; Goadrich, Mark; Rodriguez, Juan
An undergraduate laboratory activity on molecular dynamics simulations
BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 44:130-139, MAR-APR 2016
abstract, full text, DOI:10.1002/bmb.20939

Roy, Durba; Lakshminarayanan, Madhavkrishnan
Scrambling of disulfide bond scaffolds in neurotoxin AuIB: A molecular dynamics simulation study
BIOPOLYMERS, 106:196-209, MAR 2016
abstract, full text, DOI:10.1002/bip.22799

Fu, Xuegang; Zhang, Gang; Liu, Ran; Wei, Jing; Zhang-Negrerie, Daisy; Jian, Xiaodong; Gao, Qingzhi
Mechanistic Study of Human Glucose Transport Mediated by GLUT1
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 56:517-526, MAR 2016
abstract, full text, DOI:10.1021/acs.jcim.5b00597

Kapoor, Karan; McGill, Nicole; Peterson, Cynthia B.; Meyers, Harold V.; Blackburn, Michael N.; Baudry, Jerome
Discovery of Novel Nonactive Site Inhibitors of the Prothrombinase Enzyme Complex
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 56:535-547, MAR 2016
abstract, full text, DOI:10.1021/acs.jcim.5b00596

Zhang, Lei; Lei, Dongsheng; Smith, Jessica M.; Zhang, Meng; Tong, Huimin; Zhang, Xing; Lu, Zhuoyang; Liu, Jiankang; Alivisatos, A. Paul; Ren, Gang
Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography
NATURE COMMUNICATIONS, 7 Art. No. 11083, MAR 2016
abstract, full text, DOI:10.1038/ncomms11083

Laghaei, Rozita; Yu, Alan S. L.; Coalson, Rob D.
Water and ion permeability of a claudin model: A computational study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84:305-315, MAR 2016
abstract, full text, DOI:10.1002/prot.24969

Bairagya, Hridoy R.; Bansal, Manju
New insight into the architecture of oxy-anion pocket in unliganded conformation of GAT domains: A MD-simulation study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84:360-373, MAR 2016
abstract, full text, DOI:10.1002/prot.24983

Qi, Yifei; Jo, Sunhwan; Im, Wonpil
Roles of glycans in interactions between gp120 and HIV broadly neutralizing antibodies
GLYCOBIOLOGY, 26:251-260, MAR 2016
abstract, full text, DOI:10.1093/glycob/cwv101

Niinivehmas, Sanna P.; Manivannan, Elangovan; Rauhamaki, Sanna; Huuskonen, Juhani; Pentikainen, Olli T.
Identification of estrogen receptor alpha ligands with virtual screening techniques
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 64:30-39, MAR 2016
abstract, full text, DOI:10.1016/j.jmgm.2015.12.006

Barzegar, Abolfazl; Mansouri, Alireza; Azamat, Jafar
Molecular dynamics simulation of non-covalent single-walled carbon nanotube functionalization with surfactant peptides
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 64:75-84, MAR 2016
abstract, full text, DOI:10.1016/j.jmgm.2016.01.003

Arango-Lievano, Margarita; Sensoy, Ozge; Borie, Amelie; Corbani, Maithe; Guillon, Gilles; Sokoloff, Pierre; Weinstein, Harel; Jeanneteau, Freddy
A GIPC1-Palmitate Switch Modulates Dopamine Drd3 Receptor Trafficking and Signaling
MOLECULAR AND CELLULAR BIOLOGY, 36:1019-1031, MAR 2016
abstract, full text, DOI:10.1128/MCB.00916-15

Bai, Hua; Xue, Renhao; Bao, Huan; Zhang, Leili; Yethiraj, Arun; Cui, Qiang; Chapman, Edwin R.
Different states of synaptotagmin regulate evoked versus spontaneous release
NATURE COMMUNICATIONS, 7 Art. No. 10971, MAR 2016
abstract, full text, DOI:10.1038/ncomms10971

Liu, Xin; Zhang, Chen-Song; Lu, Chang; Lin, Sheng-Cai; Wu, Jia-Wei; Wang, Zhi-Xin
A conserved motif in JNK/p38-specific MAPK phosphatases as a determinant for JNK1 recognition and inactivation
NATURE COMMUNICATIONS, 7 Art. No. 10879, MAR 2016
abstract, full text, DOI:10.1038/ncomms10879

Kinde, Monica N.; Bu, Weiming; Chen, Qiang; Xu, Yan; Eckenhoff, Roderic G.; Tang, Pei
Common Anesthetic-binding Site for Inhibition of Pentameric Ligand-gated Ion Channels
ANESTHESIOLOGY, 124:664-673, MAR 2016
abstract, full text, DOI:10.1097/ALN.0000000000001005

Mahinthichaichan, Paween; Gennis, Robert B.; Tajkhorshid, Emad
All the O-2 Consumed by Thermus thermophilus Cytochrome ba(3) Is Delivered to the Active Site through a Long, Open Hydrophobic Tunnel with Entrances within the Lipid Bilayer
BIOCHEMISTRY, 55:1265-1278, MAR 1 2016
abstract, full text

Liu, Chuang; Perilla, Juan R.; Ning, Jiying; Lu, Manman; Hou, Guangjin; Ramalho, Ruben; Himes, Benjamin A.; Zhao, Gongpu; Bedwell, Gregory J.; Byeon, In-Ja; Ahn, Jinwoo; Gronenborn, Angela M.; Prevelige, Peter E.; Rousso, Itay; Aiken, Christopher; Polenova, Tatyana; Schulten, Klaus; Zhang, Peijun
Cyclophilin A stabilizes the HIV-1 capsid through a novel non-canonical binding site
NATURE COMMUNICATIONS, 7 Art. No. 10714, MAR 2016
abstract, full text, TCBG publications, DOI:10.1038/ncomms10714

Sauer, Maximilian M.; Jakob, Roman P.; Eras, Jonathan; Baday, Sefer; Eris, Deniz; Navarra, Giulio; Berneche, Simon; Ernst, Beat; Maier, Timm; Glockshuber, Rudi
Catch-bond mechanism of the bacterial adhesin FimH
NATURE COMMUNICATIONS, 7 Art. No. 10738, MAR 2016
abstract, full text, DOI:10.1038/ncomms10738

Berti, Claudio; Furini, Simone; Gillespie, Dirk
PACO: PArticle COunting Method To Enforce Concentrations in Dynamic Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:925-929, MAR 2016
abstract, full text, DOI:10.1021/acs.jctc.5b01044

Pachov, Dimitar V.; Fonseca, Rasmus; Arnol, Damien; Bernauer, Julie; van den Bedem, Henry
Coupled Motions in beta(2)AR:G alpha s Conformational Ensembles
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:946-956, MAR 2016
abstract, full text, DOI:10.1021/acs.jctc.5b00995

Ngo, Van A.; Kim, Ilsoo; Allen, Toby W.; Noskov, Sergei Y.
Estimation of Potentials of Mean Force from Nonequilibrium Pulling Simulations Using Both Minh-Adib Estimator and Weighted Histogram Analysis Method
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:1000-1010, MAR 2016
abstract, full text, DOI:10.1021/acs.jctc.5b01050

Pan, Albert C.; Weinreich, Thomas M.; Piana, Stefano; Shaw, David E.
Demonstrating an Order-of-Magnitude Sampling Enhancement in Molecular Dynamics Simulations of Complex Protein Systems
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:1360-1367, MAR 2016
abstract, full text, DOI:10.1021/acs.jctc.5b00913

Muecksch, Christian; Urbassek, Herbert M.
Accelerating Steered Molecular Dynamics: Toward Smaller Velocities in Forced Unfolding Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:1380-1384, MAR 2016
abstract, full text, DOI:10.1021/acs.jctc.5b01024

Whiteley, C. G.; Shing, C.-.Y.; Kuo, C.-.C.; Lee, Duu-Jong
Docking of HIV protease to silver nanoparticles
JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS, 60:83-91, MAR 2016
abstract, full text, DOI:10.1016/j.jtice.2015.10.029

Luan, Binquan
Radial dependence of DNA translocation velocity in a solid-state nanopore
MICROCHIMICA ACTA, 183:995-1002, MAR 2016
abstract, full text, DOI:10.1007/s00604-015-1589-2

Baltzis, Athanasios S.; Glykos, Nicholas M.
Characterizing a partially ordered miniprotein through folding molecular dynamics simulations: Comparison with the experimental data
PROTEIN SCIENCE, 25:587-596, MAR 2016
abstract, full text, DOI:10.1002/pro.2850

Aitha, Mahesh; Moller, Abraham J.; Sahu, Indra D.; Horitani, Masaki; Tierney, David L.; Crowder, Michael W.
Investigating the position of the hairpin loop in New Delhi metallo-beta-lactamase, NDM-1, during catalysis and inhibitor binding
JOURNAL OF INORGANIC BIOCHEMISTRY, 156:35-39, MAR 2016
abstract, full text, DOI:10.1016/j.jinorgbio.2015.10.011

Jung, Jaewoon; Kobayashi, Chigusa; Imamura, Toshiyuki; Sugita, Yuji
Parallel implementation of 3D FFT with volumetric decomposition schemes for efficient molecular dynamics simulations
COMPUTER PHYSICS COMMUNICATIONS, 200:57-65, MAR 2016
abstract, full text, DOI:10.1016/j.cpc.2015.10.024

Noroozi, Javad; Ghotbi, Cyrus; Sardroodi, Jaber Jahanbin; Karirni-Sabet, Javad; Robert, Marc A.
Solvation free energy and solubility of acetaminophen and ibuprofen in supercritical carbon dioxide: Impact of the solvent model
JOURNAL OF SUPERCRITICAL FLUIDS, 109:166-176, MAR 2016
abstract, full text, DOI:10.1016/j.supflu.2015.11.009

Jana, Asis K.; Tiwari, Mrityunjay K.; Vanka, Kumar; Sengupta, Neelanjana
Unraveling origins of the heterogeneous curvature dependence of polypeptide interactions with carbon nanostructures
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:5910-5924, FEB 28 2016
abstract, full text, DOI:10.1039/c5cp04675k

Sorensen, Anders B.; Madsen, Jesper J.; Svensson, L. Anders; Pedersen, Anette A.; Ostergaard, Henrik; Overgaard, Michael T.; Olsen, Ole H.; Gandhi, Prafull S.
Molecular Basis of Enhanced Activity in Factor VIIa-Trypsin Variants Conveys Insights into Tissue Factor-mediated Allosteric Regulation of Factor VIIa Activity
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:4671-4683, FEB 26 2016
abstract, full text, DOI:10.1074/jbc.M115.698613

Jana, Suvamay; Hamre, Anne Grethe; Wildberger, Patricia; Holen, Matilde Mengkrog; Eijsink, Vincent G. H.; Beckham, Gregg T.; Sorlie, Morten; Payne, Christina M.
Aromatic-Mediated Carbohydrate Recognition in Processive Serratia marcescens Chitinases
JOURNAL OF PHYSICAL CHEMISTRY B, 120:1236-1249, FEB 25 2016
abstract, full text, DOI:10.1021/acs.jpcb.8b12610

Prudovsky, Igor; Kacer, Doreen; Davis, Julie; Shah, Varun; Jayanthi, Srinivas; Huber, Isabelle; Dakshinamurthy, Rajalingam; Ganter, Owen; Soldi, Raffaella; Neivandt, David; Guvench, Olgun; Kumar, Thallapuranam Krishnaswamy Suresh
Folding of Fibroblast Growth Factor 1 Is Critical for Its Nonclassical Release
BIOCHEMISTRY, 55:1159-1167, FEB 23 2016
abstract, full text, DOI:10.1021/acs.biochem.5b01341

Zhang, Liqun; Borthakur, Susmita; Buck, Matthias
Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations
BIOPHYSICAL JOURNAL, 110:877-886, FEB 23 2016
abstract, full text, DOI:10.1016/j.bpj.2015.12.036

Patel, Dhilon S.; Re, Suyong; Wu, Emilia L.; Qi, Yifei; Klebba, Phillip E.; Widmalm, Goeran; Yeom, Min Sun; Sugita, Yuji; Im, Wonpil
Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability
BIOPHYSICAL JOURNAL, 110:930-938, FEB 23 2016
abstract, full text, DOI:10.1016/j.bpj.2016.01.002

Fuglestad, Brian; Gupta, Kushol; Wand, A. Joshua; Sharp, Kim A.
Characterization of Cetyltrimethylammonium Bromide/Hexanol Reverse Micelles by Experimentally Benchmarked Molecular Dynamics Simulations
LANGMUIR, 32:1674-1684, FEB 23 2016
abstract, full text, DOI:10.1021/acs.langmuir.5b03981

Niu, Yuzhen; Li, Shuyan; Pan, Dabo; Liu, Huanxiang; Yao, Xiaojun
Computational study on the unbinding pathways of B-RAF inhibitors and its implication for the difference of residence time: insight from random acceleration and steered molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:5622-5629, FEB 21 2016
abstract, full text, DOI:10.1039/c5cp06257h

Bai, Qifeng; Yao, Xiaojun
Investigation of allosteric modulation mechanism of metabotropic glutamate receptor 1 by molecular dynamics simulations, free energy and weak interaction analysis
SCIENTIFIC REPORTS, 6 Art. No. 21763, FEB 18 2016
abstract, full text, DOI:10.1038/srep21763

Mulholland, Sam; Turpin, Eleanor R.; Bonev, Boyan B.; Hirst, Jonathan D.
Docking and molecular dynamics simulations of the ternary complex nisin(2):lipid II
SCIENTIFIC REPORTS, 6 Art. No. 21185, FEB 18 2016
abstract, full text, DOI:10.1038/srep21185

Cai, Kaicong; Du, Fenfen; Zheng, Xuan; Liu, Jia; Zheng, Renhui; Zhao, Juan; Wang, Jianping
General Applicable Frequency Map for the Amide-I Mode in beta-Peptides
JOURNAL OF PHYSICAL CHEMISTRY B, 120:1069-1079, FEB 18 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b11643

Lang, Eric J. M.; Heyes, Logan C.; Jameson, Geoffrey B.; Parker, Emily J.
Calculated pK(a) Variations Expose Dynamic Allosteric Communication Networks
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 138:2036-2045, FEB 17 2016
abstract, full text, DOI:10.1021/jacs.5b13134

LeVine, Michael V.; Khelashvili, George; Shi, Lei; Quick, Matthias; Javitch, Jonathan A.; Weinstein, Harel
Role of Annular Lipids in the Functional Properties of Leucine Transporter LeuT Proteomicelles
BIOCHEMISTRY, 55:850-859, FEB 16 2016
abstract, full text, DOI:10.1021/acs.biochem.5b01268

Miner, Kyle D.; Kurtz, Donald M., Jr.
Active Site Metal Occupancy and Cyclic Di-GMP Phosphodiesterase Activity of Thermotoga maritima HD-GYP
BIOCHEMISTRY, 55:970-979, FEB 16 2016
abstract, full text, DOI:10.1021/acs.biochem.5b01227

Liu, Huihui; Gao, Yan-Song; Chen, Xiang-Jun; Chen, Zhe; Zhou, Hai-Meng; Yan, Yong-Bin; Gong, Haipeng
A single residue substitution accounts for the significant difference in thermostability between two isoforms of human cytosolic creatine kinase
SCIENTIFIC REPORTS, 6 Art. No. 21191, FEB 16 2016
abstract, full text, DOI:10.1038/srep21191

Ataseyer-Arslan, Belkis; Yilancioglu, Kaan; Kalkan, Zeynep; Timucin, Ahmet Can; Gur, Hazal; Isik, Fatma Busra; Deniz, Emre; Erman, Batu; Cetiner, Selim
Screening of new antileukemic agents from essential oils of algae extracts and computational modeling of their interactions with intracellular signaling nodes
EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES, 83:120-131, FEB 15 2016
abstract, full text, DOI:10.1016/j.ejps.2015.12.001

Roeland Boer, D.; Angel Ruiz-Maso, Jose; Rueda, Manuel; Petoukhov, Maxim V.; Machon, Cristina; Svergun, Dmitri I.; Orozco, Modesto; del Solar, Gloria; Coll, Miquel
Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158
SCIENTIFIC REPORTS, 6 Art. No. 20915, FEB 15 2016
abstract, full text, DOI:10.1038/srep20915

Hofmann, Sascha; Voitchovsky, Kislon; Spijker, Peter; Schmidt, Moritz; Stumpf, Thorsten
Visualising the molecular alteration of the calcite (104) - water interface by sodium nitrate
SCIENTIFIC REPORTS, 6 Art. No. 21576, FEB 15 2016
abstract, full text, DOI:10.1038/srep21576

Lavecchia, Martin J.; Puig de la Bellacasa, Raimon; Borrell, Jose I.; Cavasotto, Claudio N.
Investigating molecular dynamics-guided lead optimization of EGFR inhibitors
BIOORGANIC & MEDICINAL CHEMISTRY, 24:768-778, FEB 15 2016
abstract, full text, DOI:10.1016/j.bmc.2015.12.046

Stachiewicz, Anna; Molski, Andrzej
Diffusive dynamics of DNA unzipping in a nanopore
JOURNAL OF COMPUTATIONAL CHEMISTRY, 37:467-476, FEB 15 2016
abstract, full text, DOI:10.1002/jcc.24236

Azamat, Jafar; Balaei, Ali; Gerami, Mehdi
A theoretical study of nanostructure membranes for separating Li+ and Mg2+ from Cl-
COMPUTATIONAL MATERIALS SCIENCE, 113:66-74, FEB 15 2016
abstract, full text, DOI:10.1016/j.commatsci.2015.11.029

Elber, Ron
Perspective: Computer simulations of long time dynamics
JOURNAL OF CHEMICAL PHYSICS, 144 Art. No. 060901, FEB 14 2016
abstract, full text, DOI:10.1063/1.4940794

Sasselli, I. Ramos; Ulijn, R. V.; Tuttle, T.
CHARMM force field parameterization protocol for self-assembling peptide amphiphiles: the Fmoc moiety
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:4659-4667, FEB 14 2016
abstract, full text, DOI:10.1039/c5cp06770g

Lee, Myeongsang; Kwon, Junpyo; Na, Sungsoo
Mechanical behavior comparison of spider and silkworm silks using molecular dynamics at atomic scale
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:4814-4821, FEB 14 2016
abstract, full text, DOI:10.1039/c5cp06809f

Thomas, Michael; Corry, Ben
A computational assessment of the permeability and salt rejection of carbon nanotube membranes and their application to water desalination
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES, 374 Art. No. 20150020, FEB 13 2016
abstract, full text, DOI:10.1098/rsta.2015.0020

Ren, Jinqi; Huo, Lin; Wang, Wenjuan; Zhang, Yong; Li, Wei; Lou, Jizhong; Xu, Tao; Feng, Wei
Structural Correlation of the Neck Coil with the Coiled-coil (CC1)-Forkhead-associated (FHA) Tandem for Active Kinesin-3 KIF13A
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:3581-3594, FEB 12 2016
abstract, full text, DOI:10.1074/jbc.M115.689091

Allison, Jane R.; Lechner, Marcus; Hoeppner, Marc P.; Poole, Anthony M.
Positive Selection or Free to Vary? Assessing the Functional Significance of Sequence Change Using Molecular Dynamics
PLOS ONE, 11 Art. No. e0147619, FEB 12 2016
abstract, full text, DOI:10.1371/journal.pone.0147619

Farhi, Asaf; Singh, Bipin
Calculation of molecular free energies in classical potentials
NEW JOURNAL OF PHYSICS, 18 Art. No. 023039, FEB 11 2016
abstract, full text, DOI:10.1088/1367-2630/18/2/023039

Jin, Tiantian; Yu, Haibo; Huang, Xu-Feng
Selective binding modes and allosteric inhibitory effects of lupane triterpenes on protein tyrosine phosphatase 1B
SCIENTIFIC REPORTS, 6 Art. No. 20766, FEB 11 2016
abstract, full text, DOI:10.1038/srep20766

Martinez-Montiel, Nancy; Morales-Lara, Laura; Hernandez-Perez, Julio M.; Martinez-Contreras, Rebeca D.
In Silico Analysis of the Structural and Biochemical Features of the NMD Factor UPF1 in Ustilago maydis
PLOS ONE, 11 Art. No. e0148191, FEB 10 2016
abstract, full text, DOI:10.1371/journal.pone.0148191

Boyer, Patrick D.; Ganesh, Sairaam; Qin, Zhao; Holt, Brian D.; Buehler, Markus J.; Islam, Mohammad F.; Dahl, Kris Noel
Delivering Single-Walled Carbon Nanotubes to the Nucleus Using Engineered Nuclear Protein Domains
ACS APPLIED MATERIALS & INTERFACES, 8:3524-3534, FEB 10 2016
abstract, full text, DOI:10.1021/acsami.5b12602

Bae, Chanhyung; Anselmi, Claudio; Kalia, Jeet; Jara-Oseguera, Andres; Schwieters, Charles D.; Krepkiy, Dmitriy; Lee, Chul Won; Kim, Eun-Hee; Kim, Jae Il; Faraldo-Gomez, Jose D.; Swartz, Kenton J.
Structural insights into the mechanism of activation of the TRPV1 channel by a membrane-bound tarantula toxin
ELIFE, 5 Art. No. e11273, FEB 10 2016
abstract, full text, DOI:10.7554/elife.11273.001

Kang, Myungshim; Zhang, Pengcheng; Cui, Honggang; Loverde, Sharon M.
pi-pi Stacking Mediated Chirality in Functional Supramolecular Filaments
MACROMOLECULES, 49:994-1001, FEB 9 2016
abstract, full text, DOI:10.1021/acs.macromol.5b02148

Petridis, Loukas; Smith, Jeremy C.
Conformations of Low-Molecular-Weight Lignin Polymers in Water
CHEMSUSCHEM, 9:289-295, FEB 8 2016
abstract, full text, DOI:10.1002/cssc.201501350

Silveira, Rodrigo L.; Skaf, Munir S.
Molecular dynamics of the Bacillus subtilis expansin EXLX1: interaction with substrates and structural basis of the lack of activity of mutants
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:3510-3521, FEB 7 2016
abstract, full text, DOI:10.1039/c5cp06674c

Vogel, Alexander; Scheidt, Holger A.; Baek, Dong Jae; Bittman, Robert; Huster, Daniel
Structure and dynamics of the aliphatic cholesterol side chain in membranes as studied by H-2 NMR spectroscopy and molecular dynamics simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:3730-3738, FEB 7 2016
abstract, full text, DOI:10.1039/c5cp05084g

Ham, Sujin; Lee, Ji-Eun; Song, Suhwan; Peng, Xiaobin; Hori, Takaaki; Aratani, Naoki; Osuka, Atsuhiro; Sim, Eunji; Kim, Dongho
Direct observation of structural properties and fluorescent trapping sites in macrocyclic porphyrin arrays at the single-molecule level
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:3871-3877, FEB 7 2016
abstract, full text, DOI:10.1039/c5cp06859b

Bajaj, Harsha; Scorciapino, Mariano A.; Moynie, Lucile; Page, Malcolm G. P.; Naismith, James H.; Ceccarelli, Matteo; Winterhalter, Mathias
Molecular Basis of Filtering Carbapenems by Porins from beta-Lactam-resistant Clinical Strains of Escherichia coli
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:2837-2847, FEB 5 2016
abstract, full text, DOI:10.1074/jbc.M115.690156

Kuenze, Georg; Koehling, Sebastian; Vogel, Alexander; Rademann, Joerg; Huster, Daniel
Identification of the Glycosaminoglycan Binding Site of Interleukin-10 by NMR Spectroscopy
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:3100-3113, FEB 5 2016
abstract, full text, DOI:10.1074/jbc.M115.681759

Druart, Karen; Palmai, Zoltan; Omarjee, Eyaz; Simonson, Thomas
Protein:Ligand Binding Free Energies: A Stringent Test for Computational Protein Design
JOURNAL OF COMPUTATIONAL CHEMISTRY, 37:404-415, FEB 5 2016
abstract, full text, DOI:10.1002/jcc.24230

Chakrabarti, Mayukh; Jang, Hyunbum; Nussinov, Ruth
Comparison of the Conformations of KRAS Isoforms, K-Ras4A and K-Ras4B, Points to Similarities and Significant Differences
JOURNAL OF PHYSICAL CHEMISTRY B, 120:667-679, FEB 4 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b11110

Lee, Myeongsang; Na, Sungsoo
End Capping Alters the Structural Characteristics and Mechanical Properties of Transthyretin (105-115) Amyloid Protofibrils
CHEMPHYSCHEM, 17:425-432, FEB 3 2016
abstract, full text, DOI:10.1002/cphc.201500945

Kasuya, Go; Fujiwara, Yuichiro; Takemoto, Mizuki; Dohmae, Naoshi; Nakada-Nakura, Yoshiko; Ishitani, Ryuichiro; Hattori, Motoyuki; Nureki, Osamu
Structural Insights into Divalent Cation Modulations of ATP-Gated P2X Receptor Channels
CELL REPORTS, 14:932-944, FEB 2 2016
abstract, full text, DOI:10.1016/j.celrep.2015.12.087

Guo, Tao; Li, Haiyan; Wu, Li; Guo, Zhen; Yin, Xianzhen; Wang, Caifen; Sun, Lixin; Shao, Qun; Gu, Jingkai; York, Peter; Zhang, Jiwen
Prediction of Rate Constant for Supramolecular Systems with Multiconfigurations
JOURNAL OF PHYSICAL CHEMISTRY A, 120:981-991, FEB 2 2016
abstract, full text, DOI:10.1021/acs.jpca.5b11816

Luo, Yun; Rossi, Angelo R.; Harris, Andrew L.
Computational Studies of Molecular Permeation through Connexin26 Channels
BIOPHYSICAL JOURNAL, 110:584-599, FEB 2 2016
abstract, full text, DOI:10.1016/j.bpj.2015.11.3528

Halim, Danny; Hofstra, Robert M. W.; Signorile, Luca; Verdijk, Rob M.; van der Werf, Christine S.; Sribudiani, Yunia; Brouwer, Rutger W. W.; van IJcken, Wilfred F. J.; Dahl, Niklas; Verheij, Joke B. G. M.; Baumann, Clarisse; Kerner, John; van Bever, Yolande; Galjart, Niels; Wijnen, Rene M. H.; Tibboel, Dick; Burns, Alan J.; Muller, Franoise; Brooks, Alice S.; Alves, Maria M.
ACTG2 variants impair actin polymerization in sporadic Megacystis Microcolon Intestinal Hypoperistalsis Syndrome
HUMAN MOLECULAR GENETICS, 25:571-583, FEB 1 2016
abstract, full text, DOI:10.1093/hmg/ddv497

Simonson, Thomas; Ye-Lehmann, Shixin; Palmai, Zoltan; Amara, Najette; Wydau-Dematteis, Sandra; Bigan, Erwan; Druart, Karen; Moch, Clara; Plateau, Pierre
Redesigning the stereospecificity of tyrosyl-tRNA synthetase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84:240-253, FEB 2016
abstract, full text, DOI:10.1002/prot.24972

Louros, Nikolaos N.; Baltoumas, Fotis A.; Hamodrakas, Stavros J.; Iconomidou, Vassiliki A.
A beta-solenoid model of the Pmel17 repeat domain: insights to the formation of functional amyloid fibrils
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 30:153-164, FEB 2016
abstract, full text, DOI:10.1007/s10822-015-9892-x

Datta, Siddhartha A. K.; Clark, Patrick K.; Fan, Lixin; Ma, Buyong; Harvin, Demetria P.; Sowder, Raymond C., I.I.; Nussinov, Ruth; Wang, Yun-Xing; Rein, Alan
Dimerization of the SP1 Region of HIV-1 Gag Induces a Helical Conformation and Association into Helical Bundles: Implications for Particle Assembly
JOURNAL OF VIROLOGY, 90:1773-1787, FEB 2016
abstract, full text, DOI:10.1128/JVI.02061-15

Zhang, Dejiu; Yan, Kaige; Liu, Guangqiao; Song, Guangtao; Luo, Jiejian; Shi, Yi; Cheng, Erchao; Wu, Shan; Jiang, Taijiao; Lou, Jizhong; Gao, Ning; Qin, Yan
EF4 disengages the peptidyl-tRNA CCA end and facilitates back-translocation on the 70S ribosome
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 23:125-+, FEB 2016
abstract, full text, DOI:10.1038/nsmb.3160

Hollingsworth, Scott A.; Holden, Jeffrey K.; Li, Huiying; Poulos, Thomas L.
Elucidating nitric oxide synthase domain interactions by molecular dynamics
PROTEIN SCIENCE, 25:374-382, FEB 2016
abstract, full text, DOI:10.1002/pro.2824

Harpole, Kyle W.; O'Brien, Evan S.; Clark, Matthew A.; McKnight, C. James; Vugmeyster, Liliya; Wand, A. Joshua
The unusual internal motion of the villin headpiece subdomain
PROTEIN SCIENCE, 25:423-432, FEB 2016
abstract, full text, DOI:10.1002/pro.2831

Yu, Lili; Rodriguez, Roberto A.; Chen, L. Laurie; Chen, Liao Y.; Perry, George; McHardy, Stanton F.; Yeh, Chih-Ko
1,3-propanediol binds deep inside the channel to inhibit water permeation through aquaporins
PROTEIN SCIENCE, 25:433-441, FEB 2016
abstract, full text, DOI:10.1002/pro.2832

Cui, Dachao; Ren, Weitong; Li, Wenfei; Wang, Wei
Molecular simulations of substrate release and coupled conformational motions in adenylate kinase
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 15 Art. No. 1650004, FEB 2016
abstract, full text, DOI:10.1142/S0219633616500048

Aoun, Bachir; Russo, Daniela
Nano-confinement of biomolecules: Hydrophilic confinement promotes structural order and enhances mobility of water molecules
NANO RESEARCH, 9:273-281, FEB 2016
abstract, full text, DOI:10.1007/s12274-015-0907-7

Ngo, Thuy T. M.; Yoo, Jejoong; Dai, Qing; Zhang, Qiucen; He, Chuan; Aksimentiev, Aleksei; Ha, Taekjip
Effects of cytosine modifications on DNA flexibility and nucleosome mechanical stability
NATURE COMMUNICATIONS, 7 Art. No. 10813, FEB 2016
abstract, full text, DOI:10.1038/ncomms10813

Suzuki, Nozomu; Wang, Yichun; Elvati, Paolo; Qu, Zhi-Bei; Kim, Kyoungwon; Jiang, Shuang; Baumeister, Elizabeth; Lee, Jaewook; Yeom, Bongjun; Bahng, Joong Hwan; Lee, Jaebeom; Violi, Angela; Kotov, Nicholas A.
Chiral Graphene Quantum Dots
ACS NANO, 10:1744-1755, FEB 2016
abstract, full text, DOI:10.1021/acsnano.5b06369

DeBenedictis, Elizabeth P.; Hamed, Elham; Keten, Sinan
Mechanical Reinforcement of Proteins with Polymer Conjugation
ACS NANO, 10:2259-2267, FEB 2016
abstract, full text, DOI:10.1021/acsnano.5b06917

Cui Da-Chao; Ren Wei-Tong; Li Wen-Fei; Wang Wei
Metadynamics Simulations of Mg2+ Transfer in the Late Stage of the Adenylate Kinase Catalytic Cycle
ACTA PHYSICO-CHIMICA SINICA, 32:429-435, FEB 2016
abstract, full text, DOI:10.3866/PKU.WHXB201511201

Thomas, Trayder; Fang, Yu; Yuriev, Elizabeth; Chalmers, David K.
Ligand Binding Pathways of Clozapine and Haloperidol in the Dopamine D-2 and D-3 Receptors
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 56:308-321, FEB 2016
abstract, full text, DOI:10.1021/acs.jcim.5b00457

Giesa, Tristan; Perry, Carole C.; Buehler, Markus J.
Secondary Structure Transition and Critical Stress for a Model of Spider Silk Assembly
BIOMACROMOLECULES, 17:427-436, FEB 2016
abstract, full text, DOI:10.1021/acs.biomac.5b01246

Sun, Huiyong; Chen, Pengcheng; Li, Dan; Li, Youyong; Hou, Tingjun
Directly Binding Rather than Induced-Fit Dominated Binding Affinity Difference in (S)- and (R)-Crizotinib Bound MTH1
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:851-860, FEB 2016
abstract, full text, DOI:10.1021/acs.jctc.5b00973

Capponi, Sara; Freites, J. Alfredo; Tobias, Douglas J.; White, Stephen H.
Interleaflet mixing and coupling in liquid-disordered phospholipid bilayers
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1858:354-362, FEB 2016
abstract, full text, DOI:10.1016/j.bbamem.2015.11.024

Milenkovic, Stefan; Bondar, Ana-Nicoleta
Mechanism of conformational coupling in SecA: Key role of hydrogen-bonding networks and water interactions
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1858:374-385, FEB 2016
abstract, full text, DOI:10.1016/j.bbamem.2015.11.010

Quan, Xiaoping; Chen, Xiuqiang; Sun, Deliang; Xu, Bo; Zhao, Linlin; Shi, Xiaoqian; Liu, Hongsheng; Gao, Bing; Lu, Xiuli
The mechanism of the effect of U18666a on blocking the activity of 3 beta-hydroxysterol Delta-24-reductase (DHCR24): molecular dynamics simulation study and free energy analysis
JOURNAL OF MOLECULAR MODELING, 22 Art. No. 46, FEB 2016
abstract, full text, DOI:10.1007/s00894-016-2907-2

Li, Minghui; Kales, Stephen C.; Ma, Ke; Shoemaker, Benjamin A.; Crespo-Barreto, Juan; Cangelosi, Andrew L.; Lipkowitz, Stanley; Panchenko, Anna R.
Balancing Protein Stability and Activity in Cancer: A New Approach for Identifying Driver Mutations Affecting CBL Ubiquitin Ligase Activation
CANCER RESEARCH, 76:561-571, FEB 1 2016
abstract, full text, DOI:10.1158/0008-5472.CAN-14-3812

Cuevas-Hernandez, Roberto I.; Correa-Basurto, Jos; Flores-Sandoval, Cesar A.; Padilla-Martinez, Itzia I.; Nogueda-Torres, Benjamin; de Lourdes Villa-Tanaca, Maria; Tamay-Cach, Feliciano; Nolasco-Fidencio, Juan J.; Trujillo-Ferrara, Jose G.
Fluorine-containing benzothiazole as a novel trypanocidal agent: design, in silico study, synthesis and activity evaluation
MEDICINAL CHEMISTRY RESEARCH, 25:211-224, FEB 2016
abstract, full text, DOI:10.1007/s00044-015-1475-9

Xie, Xiao-Xiao; Li, Jun-Wei; Xiao, Shao-Ying; Liu, Yu-Zhi; Liu, Hui; Geng, Jin-Peng; Zhang, Su-Hua; Yu, Hui; Zhan, Yong; An, Hai-Long
The Structural Stability of Alpha-Helix Determined by the Preference of Amino Acids
CHINESE PHYSICS LETTERS, 33 Art. No. 028701, FEB 2016
abstract, full text, DOI:10.1088/0256-307X/33/2/028701

Das, Amit; Ghosh, Mahua; Chakrabarti, J.
Time dependent correlation between dihedral angles as probe for long range communication in proteins
CHEMICAL PHYSICS LETTERS, 645:200-204, FEB 2016
abstract, full text, DOI:10.1016/j.cplett.2015.12.060

Li, Qing; Yang, Dengfeng; Shi, Jinsheng; Xu, Xiang; Yan, Shihai; Liu, Qingzhi
Biomimetic modification of large diameter carbon nanotubes and the desalination behavior of its reverse osmosis membrane
DESALINATION, 379:164-171, FEB 1 2016
abstract, full text, DOI:10.1016/j.desal.2015.11.008

Ray, Angana; Panigrahi, Swati; Bhattacharyya, Dhananjay
A Comparison of Four Different Conformations Adopted by Human Telomeric G-Quadruplex Using Computer Simulations
BIOPOLYMERS, 105:83-99, FEB 2016
abstract, full text, DOI:10.1002/bip.22751

Aliaga, Carolina; Bravo-Moraga, Felipe; Gonzalez-Nilo, Danilo; Marquez, Sebastian; Luehr, Susan; Mena, Geraldine; Caroli Rezende, Marcos
Location of TEMPO derivatives in micelles: subtle effect of the probe orientation
FOOD CHEMISTRY, 192:395-401, FEB 1 2016
abstract, full text, DOI:10.1016/j.foodchem.2015.07.036

Sikorra, Stefan; Litschko, Christa; Mueller, Carina; Thiel, Nadine; Galli, Thierry; Eichner, Timo; Binz, Thomas
Identification and Characterization of Botulinum Neurotoxin A Substrate Binding Pockets and Their Re-Engineering for Human SNAP-23
JOURNAL OF MOLECULAR BIOLOGY, 428:372-384, JAN 29 2016
abstract, full text, DOI:10.1016/j.jmb.2015.10.024

Ricci, Clarisse G.; Silveira, Rodrigo L.; Rivalta, Ivan; Batista, Victor S.; Skaf, Munir S.
Allosteric Pathways in the PPAR gamma-RXR alpha nuclear receptor complex
SCIENTIFIC REPORTS, 6 Art. No. 19940, JAN 29 2016
abstract, full text, DOI:10.1038/srep19940

Baram, Michal; Atsmon-Raz, Yoav; Ma, Buyong; Nussinov, Ruth; Miller, Yifat
Amylin-A beta oligomers at atomic resolution using molecular dynamics simulations: a link between Type 2 diabetes and Alzheimer's disease
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:2330-2338, JAN 28 2016
abstract, full text, DOI:10.1039/c5cp03338a

Kohler, Jonatan; Schonbeck, Christian; Westh, Peter; Holm, Rene
Hydration Differences Explain the Large Variations in the Complexation Thermodynamics of Modified gamma-Cyclodextrins with Bile Salts
JOURNAL OF PHYSICAL CHEMISTRY B, 120:396-405, JAN 28 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b10536

Kitjaruwankul, Sunan; Wapeesittipan, Pattama; Boonamnaj, Panisak; Sompompisut, Pornthep
Inner and Outer Coordination Shells of Mg2+ in CorA Selectivity Filter from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 120:406-417, JAN 28 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b10925

Brock, Joseph S.; Hamberg, Mats; Balagunaseelan, Navisraj; Goodman, Michael; Morgenstern, Ralf; Strandback, Emilia; Samuelsson, Bengt; Rinaldo-Matthis, Agnes; Haeggstrom, Jesper Z.
A dynamic Asp-Arg interaction is essential for catalysis in microsomal prostaglandin E-2 synthase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 113:972-977, JAN 26 2016
abstract, full text, DOI:10.1073/pnas.1522891113

Habermacher, Chloe; Martz, Adeline; Calimet, Nicolas; Lemoine, Damien; Peverini, Laurie; Specht, Alexandre; Cecchini, Marco; Grutter, Thomas
Photo-switchable tweezers illuminate pore-opening motions of an ATP-gated P2X ion channel
ELIFE, 5 Art. No. e11050, JAN 25 2016
abstract, full text, DOI:10.7554/eLife.11050

Khantwal, Chandra M.; Abraham, Sherwin J.; Han, Wei; Jiang, Tao; Chavan, Tanmay S.; Cheng, Ricky C.; Elvington, Shelley M.; Liu, Corey W.; Mathews, Irimpan I.; Steins, Richard A.; Mchaourab, Hassane S.; Tajkhorshid, Emad; Maduke, Merritt
Revealing an outward-facing open conformational state in a CLC Cl-/H+ exchange transporter
ELIFE, 5 Art. No. e11189, JAN 22 2016
abstract, full text, DOI:10.7554/eLife.11189

Sellers, Michael S.; Hurley, Margaret M.
XPairIt Docking Protocol for peptide docking and analysis
MOLECULAR SIMULATION, 42:149-161, JAN 22 2016
abstract, full text, DOI:10.1080/08927022.2015.1025267

Dutta, Debodyuti; Mishra, Sabyashachi
Structural and mechanistic insight into substrate binding from the conformational dynamics in apo and substrate-bound DapE enzyme
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:1671-1680, JAN 21 2016
abstract, full text, DOI:10.1039/c5cp06024a

Verde, Ana Vila; Santer, Mark; Lipowsky, Reinhard
Solvent-shared pairs of densely charged ions induce intense but short-range supra-additive slowdown of water rotation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:1918-1930, JAN 21 2016
abstract, full text, DOI:10.1039/c5cp05726d

Roth, M. W.; Firlej, L.; Kuchta, B.; Connolly, M. J.; Maldonado, E.; Wexler, C.
Simulation and Characterization of Tetracosane on Graphite: Molecular Dynamics Beyond the Monolayer
JOURNAL OF PHYSICAL CHEMISTRY C, 120:984-994, JAN 21 2016
abstract, full text, DOI:10.1021/acs.jpcc.5b09677

Kritikos, Georgios; Vergadou, Niki; Economou, Ioannis G.
Molecular Dynamics Simulation of Highly Confined Glassy Ionic Liquids
JOURNAL OF PHYSICAL CHEMISTRY C, 120:1013-1024, JAN 21 2016
abstract, full text, DOI:10.1021/acs.jpcc.5b09947

Dolores Elola, M.; Rodriguez, Javier
Excess Sorption of Supercritical CO2 within Cylindrical Silica Nanopores
JOURNAL OF PHYSICAL CHEMISTRY C, 120:1262-1269, JAN 21 2016
abstract, full text, DOI:10.1021/acs.jpcc.5b09000

Pan, Qunxing; Wang, Hui; Ouyang, Wei; Wang, Xiaoli; Bi, Zhenwei; Xia, Xingxia; Wang, Yongshan; He, Kongwang
Immunogenicity of adenovirus-derived porcine parvovirus-like particles displaying B and T cell epitopes of foot-and-mouth disease
VACCINE, 34:578-585, JAN 20 2016
abstract, full text, DOI:10.1016/j.vaccine.2015.11.003

Majumdar, Sarmistha; Maiti, Satyabrata; Dastidar, Shubhra Ghosh
Dynamic and Static Water Molecules Complement the TN16 Conformational Heterogeneity inside the Tubulin Cavity
BIOCHEMISTRY, 55:335-347, JAN 19 2016
abstract, full text, DOI:10.1021/acs.biochem.5b00853

Bowerman, Samuel; Wereszczynski, Jeff
Effects of MacroH2A and H2A.Z on Nucleosome Dynamics as Elucidated by Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 110:327-337, JAN 19 2016
abstract, full text, DOI:10.1016/j.bpj.2015.12.015

Shaytan, Alexey K.; Armeev, Grigoriy A.; Goncearenco, Alexander; Zhurkin, Victor B.; Landsman, David; Panchenko, Anna R.
Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions
JOURNAL OF MOLECULAR BIOLOGY, 428:221-237, JAN 16 2016
abstract, full text, DOI:10.1016/j.jmb.2015.12.004

Zhang, Qi-Lin; Yang, Rong-Yao
Fast transport of water molecules across carbon nanotubes induced by static electric fields
CHEMICAL PHYSICS LETTERS, 644:201-204, JAN 16 2016
abstract, full text, DOI:10.1016/j.cplett.2015.11.061

Hanson, M. Gartz; Aiken, Jayne; Sietsema, Daniel V.; Sept, David; Bates, Emily A.; Niswander, Lee; Moore, Jeffrey K.
Novel alpha-tubulin mutation disrupts neural development and tubulin proteostasis
DEVELOPMENTAL BIOLOGY, 409:406-419, JAN 15 2016
abstract, full text, DOI:10.1016/j.ydbio.2015.11.022

Musille, Paul M.; Kossmann, Bradley R.; Kohn, Jeffrey A.; Ivanov, Ivaylo; Ortlund, Eric A.
Unexpected Allosteric Network Contributes to LRH-1 Co-regulator Selectivity
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:1411-1426, JAN 15 2016
abstract, full text

Tavoulari, Sotiria; Margheritis, Eleonora; Nagarajan, Anu; DeWitt, David C.; Zhang, Yuan-Wei; Rosado, Edwin; Ravera, Silvia; Rhoades, Elizabeth; Forrest, Lucy R.; Rudnick, Gary
Two Na+ Sites Control Conformational Change in a Neurotransmitter Transporter Homolog
JOURNAL OF BIOLOGICAL CHEMISTRY, 291:1456-1471, JAN 15 2016
abstract, full text

Ingolfsson, Helgi I.; Arnarez, Clement; Periole, Xavier; Marrink, Siewert J.
Computational 'microscopy' of cellular membranes
JOURNAL OF CELL SCIENCE, 129:257-268, JAN 15 2016
abstract, full text, DOI:10.1242/jcs.176040

Zygmunt, William; Potoff, Jeffrey J.
The effect of fluorination on the physical properties and the free energies of hydration of 1-alcohols
FLUID PHASE EQUILIBRIA, 407:314-321, JAN 15 2016
abstract, full text, DOI:10.1016/j.fluid.2015.07.005

Zanuy, David; Poater, Jordi; Sola, Miquel; Hamley, Ian W.; Aleman, Carlos
Fmoc-RGDS based fibrils: atomistic details of their hierarchical assembly
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:1265-1278, JAN 14 2016
abstract, full text, DOI:10.1039/c5cp04269k

Irudayanathan, Flaviyan Jerome; Trasatti, John P.; Karande, Pankaj; Nangia, Shikha
Molecular Architecture of the Blood Brain Barrier Tight Junction Proteins-A Synergistic Computational and In Vitro Approach
JOURNAL OF PHYSICAL CHEMISTRY B, 120:77-88, JAN 14 2016
abstract, full text, DOI:10.1021/acs.jpcb.5b09977

Poblete, Horacio; Agarwal, Anirudh; Thomas, Suma S.; Bohne, Cornelia; Ravichandran, Ranjithkumar; Phospase, Jaywant; Comer, Jeffrey; Alarcon, Emilio I.
New Insights into Peptide-Silver Nanoparticle Interaction: Deciphering the Role of Cysteine and Lysine in the Peptide Sequence
LANGMUIR, 32:265-273, JAN 12 2016
abstract, full text, DOI:10.1021/acs.langmuir.5b03601

Zielinska, Joanna; Wieczor, Milosz; Baczek, Tomasz; Gruszecki, Marcin; Czub, Jacek
Thermodynamics and kinetics of amphotericin B self-association in aqueous solution characterized in molecular detail
SCIENTIFIC REPORTS, 6 Art. No. 19109, JAN 8 2016
abstract, full text, DOI:10.1038/srep19109

Krzeminska, A.; Swiderek, K. P.; Paneth, P.
Theoretical studies of energetics and binding isotope effects of binding a triazole-based inhibitor to HIV-1 reverse transcriptase
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18:310-317, JAN 7 2016
abstract, full text, DOI:10.1039/c5cp06050h

Au, Loretta; Green, David F.
Direct Calculation of Protein Fitness Landscapes through Computational Protein Design
BIOPHYSICAL JOURNAL, 110:75-84, JAN 5 2016
abstract, full text, DOI:10.1016/j.bpj.2015.11.029

Juvonen, Risto O.; Kuusisto, Mira; Fohrgrup, Carolin; Pitkanen, Mari H.; Nevalainen, Tapio J.; Auriola, Seppo; Raunio, Hannu; Pasanen, Markku; Pentikainen, Olli T.
Inhibitory effects and oxidation of 6-methylcoumarin, 7-methylcoumarin and 7-formylcoumarin via human CYP2A6 and its mouse and pig orthologous enzymes
XENOBIOTICA, 46:14-24, JAN 2 2016
abstract, full text, DOI:10.3109/00498254.2015.1048327

Haq, Imran; Irving, James A.; Saleh, Aarash D.; Dron, Louis; Regan-Mochrie, Gemma L.; Motamedi-Shad, Neda; Hurst, John R.; Gooptu, Bibek; Lomas, David A.
Deficiency Mutations of Alpha-1 Antitrypsin Effects on Folding, Function, and Polymerization
AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY, 54:71-80, JAN 2016
abstract, full text, DOI:10.1165/rcmb.2015-0154OC

Ljubetic, A.; Drobnak, I.; Gradisar, H.; Jerala, R.
Designing the structure and folding pathway of modular topological bionanostructures
CHEMICAL COMMUNICATIONS, 52:5220-5229, 2016
abstract, full text, DOI:10.1039/c6cc00421k

Nevidimov, A. V.; Razumov, V. F.
Computer Simulation of Ligand Shells of Colloidal Cadmium Selenide Quantum Dots
COLLOID JOURNAL, 78:83-89, JAN 2016
abstract, full text, DOI:10.1134/S1061933X16010129

Karandur, D.; Pettitt, B. M.
The contribution of electrostatic interactions to the collapse of oligoglycine in water
CONDENSED MATTER PHYSICS, 19 Art. No. 23802, 2016
abstract, full text, DOI:10.5488/CMP.19.23802

Brasili, Davide; Watly, Joanna; Simonovsky, Eyal; Guerrini, Remo; Barbosa, Nuno A.; Wieczorek, Robert; Remelli, Maurizio; Kozlowski, Henryk; Miller, Yifat
The unusual metal ion binding ability of histidyl tags and their mutated derivatives
DALTON TRANSACTIONS, 45:5629-5639, 2016
abstract, full text, DOI:10.1039/c5dt04747a

Verma, Saroj; Pandey, Shashi; Agarwal, Pooja; Verma, Pravesh; Deshpande, Shreekant; Saxena, Jitendra Kumar; Srivastava, Kumkum; Chauhan, Prem M. S.; Prabhakar, Yenamandra S.
N-(7-Chloroquinolinyl-4-aminoalkyl)arylsulfonamides as antimalarial agents: rationale for the activity with reference to inhibition of hemozoin formation
RSC ADVANCES, 6:25584-25593, 2016
abstract, full text, DOI:10.1039/c6ra00846a

Chatterjee, Prathit; Sengupta, Neelanjana
Signatures of protein thermal denaturation and local hydrophobicity in domain specific hydration behavior: a comparative molecular dynamics study
MOLECULAR BIOSYSTEMS, 12:1139-1150, 2016
abstract, full text, DOI:10.1039/c6mb00017g

Yang, Chao; Zhang, Shilei; Bai, Zhengya; Hou, Shasha; Wu, Di; Huang, Jian; Zhou, Peng
A two-step binding mechanism for the self-binding peptide recognition of target domains
MOLECULAR BIOSYSTEMS, 12:1201-1213, 2016
abstract, full text, DOI:10.1039/c5mb00800j

Han, Dan; Su, Min; Tan, Jianjun; Li, Chunhua; Zhang, Xiaoyi; Wang, Cunxin
Structure-activity relationship and binding mode studies for a series of diketo-acids as HIV integrase inhibitors by 3D-QSAR, molecular docking and molecular dynamics simulations
RSC ADVANCES, 6:27594-27606, 2016
abstract, full text, DOI:10.1039/c6ra00713a

Garrido-Acosta, Osvaldo; Meza-Toledo, Sergio E.; Anguiano-Robledo, Liliana; Soriano-Ursua, Marvin A.; Correa-Basurto, Jose; Davood, Asghar; Chamorro-Cevallos, German
Anticonvulsant and Toxicological Evaluation of Parafluorinated/Chlorinated Derivatives of 3-Hydroxy-3-ethyl-3-phenylpropionamide
BIOMED RESEARCH INTERNATIONAL, Art. No. 3978010, 2016
abstract, full text, DOI:10.1155/2016/3978010

Yu, Alvin; Wied, Tyler; Belcher, John; Lau, Albert Y.
Computing Conformational Free Energies of iGluR Ligand-Binding Domains
IONOTROPIC GLUTAMATE RECEPTOR TECHNOLOGIES, 119-132, 2016
abstract, full text, DOI:10.1007/978-1-4939-2812-5_9

Xu, Lei; Li, Dan; Tao, Li; Yang, Yanling; Li, Youyong; Hou, Tingjun
Binding mechanisms of 1,4-dihydropyridine derivatives to L-type calcium channel Ca(v)1.2: a molecular modeling study
MOLECULAR BIOSYSTEMS, 12:379-390, 2016
abstract, full text, DOI:10.1039/c5mb00781j

Sikdar, Samapan; Chakrabarti, J.; Ghosh, Mahua
Conformational thermodynamics guided structural reconstruction of biomolecular fragments
MOLECULAR BIOSYSTEMS, 12:444-453, 2016
abstract, full text, DOI:10.1039/c5mb00529a

Espinoza-Fonseca, L. Michel
Pathogenic mutation R959W alters recognition dynamics of dysferlin inner DysF domain
MOLECULAR BIOSYSTEMS, 12:973-981, 2016
abstract, full text, DOI:10.1039/c5mb00772k

Jang, Hyunbum; Arce, Fernando Teran; Lee, Joon; Gillman, Alan L.; Ramachandran, Srinivasan; Kagan, Bruce L.; Lal, Ratnesh; Nussinov, Ruth
Computational Methods for Structural and Functional Studies of Alzheimer's Amyloid Ion Channels
PROTEIN AMYLOID AGGREGATION: METHODS AND PROTOCOLS, 1345:251-268, 2016
abstract, full text, DOI:10.1007/978-1-4939-2978-8_16

Jo, Sunhwan; Qi, Yifei; Im, Wonpil
Preferred conformations of N-glycan core pentasaccharide in solution and in glycoproteins
GLYCOBIOLOGY, 26:19-29, JAN 2016
abstract, full text, DOI:10.1093/glycob/cwv083

Luan, Binquan; Tien Huynh; Zhou, Ruhong
Complete wetting of graphene by biological lipids
NANOSCALE, 8:5750-5754, 2016
abstract, full text, DOI:10.1039/c6nr00202a

Gupta, Prashant Kumar; Meuwly, Markus
Ligand and interfacial dynamics in a homodimeric hemoglobin
STRUCTURAL DYNAMICS, 3 Art. No. 012003, JAN 2016
abstract, full text, DOI:10.1063/1.4940228

Baskin, Artem; Kral, Petr
Hybrid Modeling of Molecular Sensing and Catalysis in Low-dimensional Nanomaterials
MATERIALS TODAY-PROCEEDINGS, 3:396-410, 2016
abstract, full text, DOI:10.1016/j.matpr.2016.01.027

Moreira, Ines P.; Sasselli, Ivan Ramos; Cannon, Daniel A.; Hughes, Meghan; Lamprou, Dimitrios A.; Tuttle, Tell; Ulijn, Rein V.
Enzymatically activated emulsions stabilised by interfacial nanofibre networks
SOFT MATTER, 12:2623-2631, 2016
abstract, full text, DOI:10.1039/c5sm02730f

Russ, K. A.; Elvati, P.; Parsonage, T. L.; Dews, A.; Jarvis, J. A.; Ray, M.; Schneider, B.; Smith, P. J. S.; Williamson, P. T. F.; Violi, A.; Philbert, M. A.
C-60 fullerene localization and membrane interactions in RAW 264.7 immortalized mouse macrophages
NANOSCALE, 8:4134-4144, 2016
abstract, full text, DOI:10.1039/c5nr07003a

Zhao, Lina; Zhai, Jiao; Zhang, Xuejie; Gao, Xueyun; Fang, Xiaohong; Li, Jingyuan
Computational design of peptide-Au cluster probe for sensitive detection of alpha(IIb)beta(3) integrin
NANOSCALE, 8:4203-4208, 2016
abstract, full text, DOI:10.1039/c5nr09175f

St-Jacques, Antony D.; Rachel, Natalie M.; Curry, Dan R.; Gillett, Steve M. F. G.; Clouthier, Christopher M.; Keillor, Jeffrey W.; Pelletier, Joelle N.; Chica, Roberto A.
Specificity of transglutaminase-catalyzed peptide synthesis
JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, 123:53-61, JAN 2016
abstract, full text, DOI:10.1016/j.molcatb.2015.11.009

Pino-Angeles, Almudena; Leveritt, John M., I.I.I.; Lazaridis, Themis
Pore Structure and Synergy in Antimicrobial Peptides of the Magainin Family
PLOS COMPUTATIONAL BIOLOGY, 12 Art. No. e1004570, JAN 2016
abstract, full text, DOI:10.1371/journal.pcbi.1004570

Van Ngo; Wang, Yibo; Haas, Stephan; Noskov, Sergei Y.; Farley, Robert A.
K+ Block Is the Mechanism of Functional Asymmetry in Bacterial Na-v Channels
PLOS COMPUTATIONAL BIOLOGY, 12 Art. No. e1004482, JAN 2016
abstract, full text, DOI:10.1371/journal.pcbi.1004482

Karandur, Deepti; Harris, Robert C.; Pettitt, B. Montgomery
Protein collapse driven against solvation free energy without H-bonds
PROTEIN SCIENCE, 25:103-110, JAN 2016
abstract, full text, DOI:10.1002/pro.2749

Hua, Duy P.; Huang, He; Roy, Amitava; Post, Carol Beth
Evaluating the dynamics and electrostatic interactions of folded proteins in implicit solvents
PROTEIN SCIENCE, 25:204-218, JAN 2016
abstract, full text, DOI:10.1002/pro.2753

Timucin, Emel; Cousido-Siah, Alexandra; Mitschler, Andre; Podjarny, Alberto; Sezerman, Osman Ugur
Probing the roles of two tryptophans surrounding the unique zinc coordination site in lipase family I.5
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 84:129-142, JAN 2016
abstract, full text, DOI:10.1002/prot.24961

Dhakal, Soma; Adendorff, Matthew R.; Liu, Minghui; Yan, Hao; Bathe, Mark; Walter, Nils G.
Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis
NANOSCALE, 8:3125-3137, 2016
abstract, full text, DOI:10.1039/c5nr07263h

Lehtonen, Soili I.; Tullila, Antti; Agrawal, Nitin; Kukkurainen, Sampo; Kahkonen, Niklas; Koskinen, Masi; Nevanen, Tarja K.; Johnson, Mark S.; Airenne, Tomi T.; Kulomaa, Markku S.; Riihimaki, Tiina A.; Hytonen, Vesa P.
Artificial Avidin-Based Receptors for a Panel of Small Molecules
ACS CHEMICAL BIOLOGY, 11:211-221, JAN 2016
abstract, full text, DOI:10.1021/acschembio.5b00906

Atsmon-Raz, Yoav; Miller, Yifat
Non-Amyloid-beta Component of Human alpha-Synuclein Oligomers Induces Formation of New A beta Oligomers: Insight into the Mechanisms That Link Parkinson's and Alzheimer's Diseases
ACS CHEMICAL NEUROSCIENCE, 7:46-55, JAN 2016
abstract, full text, DOI:10.1021/acs.chemneuro.5b00204

Wilkens, Casper; Auger, Kyle D.; Anderson, Nolan T.; Meekins, David A.; Raththagala, Madushi; Abou Hachem, Maher; Payne, Christina M.; Gentry, Matthew S.; Svensson, Birte
Plant -glucan phosphatases SEX4 and LSF2 display different affinity for amylopectin and amylose
FEBS LETTERS, 590:118-128, JAN 2016
abstract, full text, DOI:10.1002/1873-3468.12027

Autzen, Henriette Elisabeth; Musgaard, Maria
MD Simulations of P-Type ATPases in a Lipid Bilayer System
P-TYPE ATPASES: METHODS AND PROTOCOLS, 1377:459-492, 2016
abstract, full text, DOI:10.1007/978-1-4939-3179-8_40

Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna
Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics
JOURNAL OF MOLECULAR MODELING, 22 Art. No. 20, JAN 2016
abstract, full text, DOI:10.1007/s00894-015-2881-0

Xu, W.; Lan, Z.; Peng, B. L.; Wen, R. F.; Ma, X. H.
Effect of nano structures on the nucleus wetting modes during water vapour condensation: from individual groove to nano-array surface
RSC ADVANCES, 6:7923-7932, 2016
abstract, full text, DOI:10.1039/c5ra23836f

Chaves, Silvina; Pera, Licia M.; Luis Avila, Cesar; Romero, Cintia M.; Baigori, Mario; Moran Vieyra, F. Eduardo; Borsarelli, Claudio D.; Chehin, Rosana N.
Towards efficient biocatalysts: photo-immobilization of a lipase on novel lysozyme amyloid-like nanofibrils
RSC ADVANCES, 6:8528-8538, 2016
abstract, full text, DOI:10.1039/c5ra19590j

Luan, Binquan; Huynh, Tien; Li, Jingyuan; Zhout, Ruhong
Nanomechanics of Protein Unfolding Outside a Generic Nanopore
ACS NANO, 10:317-323, JAN 2016
abstract, full text, DOI:10.1021/acsnano.5b04557

Dequidt, Alain; Devemy, Julien; Padua, Agilio A. H.
Thermalized Drude Oscillators with the LAMMPS Molecular Dynamics Simulator
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 56:260-268, JAN 2016
abstract, full text, DOI:10.1021/acs.jcim.5b00612

Zhang, Qi-Lin; Yang, Rong-Yao; Jiang, Wei-Zhou; Huang, Zi-Qian
Fast water channeling across carbon nanotubes in far infrared terahertz electric fields
NANOSCALE, 8:1886-1891, 2016
abstract, full text, DOI:10.1039/c5nr07281f

Bagci, Eyup; Aydin, Emel; Mihasan, Marius; Maniu, Calin; Hritcu, Lucian
Anxiolytic and antidepressant-like effects of Ferulago angulata essential oil in the scopolamine rat model of Alzheimer's disease
FLAVOUR AND FRAGRANCE JOURNAL, 31:70-80, JAN 2016
abstract, full text, DOI:10.1002/ffj.3289

Chan, Chun; Wen, Haohua; Lu, Lanyuan; Fan, Jun
Multiscale molecular dynamics simulations of membrane remodeling by Bin/Amphiphysin/Rvs family proteins
CHINESE PHYSICS B, 25 Art. No. 018707, JAN 2016
abstract, full text, DOI:10.1088/1674-1056/25/1/018707

Kotar, Anita; Tomasic, Tihomir; Zivkovic, Martina Lenarcic; Jug, Gregor; Plavec, Janez; Anderluh, Marko
STD NMR and molecular modelling insights into interaction of novel mannose-based ligands with DC-SIGN
ORGANIC & BIOMOLECULAR CHEMISTRY, 14:862-875, 2016
abstract, full text, DOI:10.1039/c5ob01916h

Borreguero, Jose M.; Lynch, Vickie E.
Molecular Dynamics Force-Field Refinement against Quasi-Elastic Neutron Scattering Data
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:9-17, JAN 2016
abstract, full text, DOI:10.1021/acs.jctc.5b00878

Sedeh, Reza Sharifi; Pan, Keyao; Adendorff, Matthew Ralph; Hallatschek, Oskar; Bathe, Klaus-Juergen; Bathe, Mark
Computing Nonequilibrium Conformational Dynamics of Structured Nucleic Acid Assemblies
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:261-273, JAN 2016
abstract, full text, DOI:10.1021/acs.jctc.5b00965

Lee, Jumin; Cheng, Xi; Swails, Jason M.; Yeom, Min Sun; Eastman, Peter K.; Lemkul, Justin A.; Wei, Shuai; Buckner, Joshua; Jeong, Jong Cheol; Qi, Yifei; Jo, Sunhwan; Pande, Vijay S.; Case, David A.; Brooks, Charles L., I.I.I.; MacKerell, Alexander D., Jr.; Klauda, Jeffery B.; Im, Wonpil
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:405-413, JAN 2016
abstract, full text, DOI:10.1021/acs.jctc.5b00935

Yoo, Jejoong; Aksimentiev, Aleksei
Improved Parameterization of Amine-Carboxylate and Amine-Phosphate Interactions for Molecular Dynamics Simulations Using the CHARMM and AMBER Force Fields
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12:430-443, JAN 2016
abstract, full text, DOI:10.1021/acs.jctc.5b00967

Cosenza, Chiara; Lettera, Vincenzo; Causa, Filippo; Scognamiglio, Pasqualina Liana; Battista, Edmondo; Netti, Paolo Antonio
Cell mechanosensory recognizes ligand compliance at biomaterial interface
BIOMATERIALS, 76:282-291, JAN 2016
abstract, full text, DOI:10.1016/j.biomaterials.2015.10.068

Huang, Zi-Qian; Yang, Rong-Yao; Jiang, Wei-Zhou; Zhang, Qi-Lin
Heating of Nanosized Liquid Water in High-Intensity Terahertz Pulses
CHINESE PHYSICS LETTERS, 33 Art. No. 013101, JAN 2016
abstract, full text, DOI:10.1088/0256-307X/33/1/013101

Yu, Xiaofeng; Nandekar, Prajwal; Mustafa, Ghulam; Cojocaru, Vlad; Lepesheva, Galina I.; Wade, Rebecca C.
Ligand tunnels in T-brucei and human CYP51: Insights for parasite-specific drug design
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1860:67-78, JAN 2016
abstract, full text, DOI:10.1016/j.bbagen.2015.10.015

Schadzek, Patrik; Schlingmann, Barbara; Schaarschmidt, Frank; Lindner, Julia; Koval, Michael; Heisterkamp, Alexander; Preller, Matthias; Ngezahayo, Anaclet
The cataract related mutation N188T in human connexin46 (hCx46) revealed a critical role for residue N188 in the docking process of gap junction channels
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1858:57-66, JAN 2016
abstract, full text, DOI:10.1016/j.bbamem.2015.10.001

Morrison, Lindsay J.; Brodbelt, Jennifer S.
Charge site assignment in native proteins by ultraviolet photodissociation (UVPD) mass spectrometry
ANALYST, 141:166-176, 2016
abstract, full text, DOI:10.1039/c5an01819f

Liu, Peng; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng
The true nature of rotary movements in rotaxanes
CHEMICAL SCIENCE, 7:457-462, 2016
abstract, full text, DOI:10.1039/c5sc03022f

Bergmann, Myriam; Michaud, Gaelle; Visini, Ricardo; Jin, Xian; Gillon, Emilie; Stocker, Achim; Imberty, Anne; Darbre, Tamis; Reymond, Jean-Louis
Multivalency effects on Pseudomonas aeruginosa biofilm inhibition and dispersal by glycopeptide dendrimers targeting lectin LecA
ORGANIC & BIOMOLECULAR CHEMISTRY, 14:138-148, 2016
abstract, full text, DOI:10.1039/c5ob01682g

Korchowiec, Beata; Gorczyca, Marcelina; Rogalska, Ewa; Regnouf-de-Vains, Jean-Bernard; Mourer, Maxime; Korchowiec, Jacek
The selective interactions of cationic tetra-p-guanidinoethylcalix[4]arene with lipid membranes: theoretical and experimental model studies
SOFT MATTER, 12:181-190, 2016
abstract, full text, DOI:10.1039/c5sm01891a

Shahbaaz, Mohd.; Bisetty, Krishna; Ahmad, Faizan; Hassan, Md. Imtaiyaz
Current Advances in the Identification and Characterization of Putative Drug and Vaccine Targets in the Bacterial Genomes
CURRENT TOPICS IN MEDICINAL CHEMISTRY, 16:1040-1069, 2016
abstract, full text, DOI:10.2174/1568026615666150825143307

Hosek, Petr; Spiwok, Vojtech
Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics
COMPUTER PHYSICS COMMUNICATIONS, 198:222-229, JAN 2016
abstract, full text, DOI:10.1016/j.cpc.2015.08.037

Picaud, Fabien; Boukari, Khaoula; Balme, Sebastien; Janot, Jean Marc; Henn, Francois
Selectivity against proton in cation permeable hybrid solid state membrane
COMPUTATIONAL MATERIALS SCIENCE, 111:380-386, JAN 2016
abstract, full text, DOI:10.1016/j.commatsci.2015.09.044

Harrach, Michael F.; Drossel, Barbara; Winschel, Wadim; Gutmann, Torsten; Buntkowsky, Gerd
Mixtures of Isobutyric Acid and Water Confined in Cylindrical Silica Nanopores Revisited: A Combined Solid-State NMR and Molecular Dynamics Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY C, 119:28961-28969, DEC 31 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b09537

Spellmon, Nicholas; Sun, Xiaonan; Sirinupong, Nualpun; Edwards, Brian; Li, Chunying; Yang, Zhe
Molecular Dynamics Simulation Reveals Correlated Inter-Lobe Motion in Protein Lysine Methyltransferase SMYD2
PLOS ONE, 10 Art. No. e0145758, DEC 30 2015
abstract, full text, DOI:10.1371/journal.pone.0145758

Gur, Mert; Zomot, Elia; Cheng, Mary Hongying; Bahar, Ivet
Energy landscape of LeuT from molecular simulations
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 243134, DEC 28 2015
abstract, full text, DOI:10.1063/1.4936133

MacDermaid, Christopher M.; Kashyap, Hemant K.; DeVane, Russell H.; Shinoda, Wataru; Klauda, Jeffery B.; Klein, Michael L.; Fiorin, Giacomo
Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes
JOURNAL OF CHEMICAL PHYSICS, 143, DEC 28 2015
abstract, full text, DOI:10.1063/1.4937153

Wei, Zonghui; Luijten, Erik
Systematic coarse-grained modeling of complexation between small interfering RNA and polycations
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 243146, DEC 28 2015
abstract, full text, DOI:10.1063/1.4937384

Yu, Hang; Han, Wei; Ma, Wen; Schulten, Klaus
Transient beta-hairpin formation in alpha-synuclein monomer revealed by coarse-grained molecular dynamics simulation
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 243142, DEC 28 2015
abstract, full text, TCBG publications, DOI:10.1063/1.4936910

Gorham, Ronald D., Jr.; Nunez, Vicente; Lin, Jung-Hsin; Rooijakkers, Suzan H. M.; Vullev, Valentine I.; Morikis, Dirnitrios
Discovery of Small Molecules for Fluorescent Detection of Complement Activation Product C3d
JOURNAL OF MEDICINAL CHEMISTRY, 58:9535-9545, DEC 24 2015
abstract, full text, DOI:10.1021/acs.jmedchem.5b01062

Palese, Luigi L.
Correlation Analysis of Trp-Cage Dynamics in Folded and Unfolded States
JOURNAL OF PHYSICAL CHEMISTRY B, 119:15568-15573, DEC 24 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b09678

Lemkul, Justin A.; Huang, Jing; MacKerell, Alexander D., Jr.
Induced Dipole-Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid beta-Peptides
JOURNAL OF PHYSICAL CHEMISTRY B, 119:15574-15582, DEC 24 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b09978

Song, Yang; Nelp, Micah T.; Bandarian, Vahe; Wysocki, Vicki H.
Refining the Structural Model of a Heterohexameric Protein Complex: Surface Induced Dissociation and Ion Mobility Provide Key Connectivity and Topology Information
ACS CENTRAL SCIENCE, 1:477-487, DEC 23 2015
abstract, full text, DOI:10.1021/acscentsci.5b00251

Nickels, Jonathan D.; Cheng, Xiaolin; Mostofian, Barmak; Stanley, Christopher; Lindner, Benjamin; Heberle, Frederick A.; Perticaroli, Stefania; Feirgenson, Mikhail; Egami, Takeshi; Standaert, Robert F.; Smith, Jeremy C.; Myles, Dean A. A.; Ohl, Michael; Katsaras, John
Mechanical Properties of Nanoscopic Lipid Domains
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:15772-15780, DEC 23 2015
abstract, full text, DOI:10.1021/jacs.5b08894

Sjulstok, Emil; Olsen, Jogvan Magnus Haugaard; Solov'yov, Ilia A.
Quantifying electron transfer reactions in biological systems: what interactions play the major role?
SCIENTIFIC REPORTS, 5 Art. No. 18446, DEC 22 2015
abstract, full text, DOI:10.1038/srep18446

Basu, Ipsita; Manna, Moutusi; Mukhopadhyay, Chaitali
Insights into the behavioral difference of water in the presence of GM1
FEBS LETTERS, 589:3887-3892, DEC 21 2015
abstract, full text, DOI:10.1016/j.febslet.2015.11.014

Simonin, Alexandre; Montalbetti, Nicolas; Gyimesi, Gergely; Pujol-Gimenez, Jonai; Hediger, Matthias A.
The Hydroxyl Side Chain of a Highly Conserved Serine Residue Is Required for Cation Selectivity and Substrate Transport in the Glial Glutamate Transporter GLT-1/SLC1A2
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:30464-30474, DEC 18 2015
abstract, full text, DOI:10.1074/jbc.M115.689836

Niu, Yuzhen; Pan, Dabo; Shi, Danfeng; Bai, Qifeng; Liu, Huanxiang; Yao, Xiaojun
Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations
PLOS ONE, 10 Art. No. e0145219, DEC 17 2015
abstract, full text, DOI:10.1371/journal.pone.0145219

Jarvis, S. P.; Taylor, S.; Baran, J. D.; Thompson, D.; Saywell, A.; Mangham, B.; Champness, N. R.; Larsson, J. A.; Moriarty, P.
Physisorption Controls the Conformation and Density of States of an Adsorbed Porphyrin
JOURNAL OF PHYSICAL CHEMISTRY C, 119:27982-27994, DEC 17 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b08350

Walters, Peter L.; Makri, Nancy
Quantum-Classical Path Integral Simulation of Ferrocene-Ferrocenium Charge Transfer in Liquid Hexane
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:4959-4965, DEC 17 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b02265

Batista, Mariana R. B.; Martinez, Leandro
Conformational Diversity of the Helix 12 of the Ligand Binding Domain of PPAR gamma and Functional Implications
JOURNAL OF PHYSICAL CHEMISTRY B, 119:15418-15429, DEC 17 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b09824

Wang, Jianping; Yang, Fan; Zhao, Juan
Selectively Probing the Structures and Dynamics of beta-Peptide Aggregates Using the Amide-A Vibrational Marker
JOURNAL OF PHYSICAL CHEMISTRY B, 119:15451-15459, DEC 17 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b10249

Villarreal, Oscar D.; Chen, Liao Y.; Whetten, Robert L.; Demeler, Borries
Aspheric Solute Ions Modulate Gold Nanoparticle Interactions in an Aqueous Solution: An Optimal Way To Reversibly Concentrate Functionalized Nanoparticles
JOURNAL OF PHYSICAL CHEMISTRY B, 119:15502-15508, DEC 17 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b09864

Jin, Xiaojie; Bai, Qifeng; Xue, Weiwei; Liu, Huanxiang; Yao, Xiaojun
Computational study on the inhibition mechanism of a cyclic peptide MaD5 to PfMATE: Insight from molecular dynamics simulation, free energy calculation and dynamical network analysis
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 149:81-88, DEC 15 2015
abstract, full text, DOI:10.1016/j.chemolab.2015.10.013

Fields, James B.; Hollingsworth, Scott A.; Chreifi, Georges; Heyden, Matthias; Arce, Anton P.; Magana-Garcia, Hugo I.; Poulos, Thomas L.; Tobias, Douglas J.
"Bind and Crawl" Association Mechanism of Leishmania major Peroxidase and Cytochrome c Revealed by Brownian and Molecular Dynamics Simulations
BIOCHEMISTRY, 54:7272-7282, DEC 15 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00569

Hamre, Anne Grethe; Jana, Suvamay; Reppert, Nicole K.; Payne, Christina M.; Sorlie, Morten
Processivity, Substrate Positioning, and Binding: The Role of Polar Residues in a Family 18 Glycoside Hydrolase
BIOCHEMISTRY, 54:7292-7306, DEC 15 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00830

Chavan, Tanmay S.; Jang, Hyunbum; Khavrutskii, Lyuba; Abraham, Sherwin J.; Banerjee, Avik; Freed, Benjamin C.; Johannessen, Liv; Tarasov, Sergey G.; Gaponenko, Vadim; Nussinov, Ruth; Tarasova, Nadya I.
High-Affinity Interaction of the K-Ras4B Hypervariable Region with the Ras Active Site
BIOPHYSICAL JOURNAL, 109:2602-2613, DEC 15 2015
abstract, full text, DOI:10.1016/j.bpj.2015.09.034

Chen, Cong; Zhang, Ning; Li, Weizhong; Song, Yongchen
Water Contact Angle Dependence with Hydroxyl Functional Groups on Silica Surfaces under CO2 Sequestration Conditions
ENVIRONMENTAL SCIENCE & TECHNOLOGY, 49:14680-14687, DEC 15 2015
abstract, full text, DOI:10.1021/acs.est.5b03646

Agullo, Luis; Malhotra, Sunny; Fissolo, Nicolas; Montalban, Xavier; Comabella, Manuel
Molecular dynamics and intracellular signaling of the TNF-R1 with the R92Q mutation
JOURNAL OF NEUROIMMUNOLOGY, 289:12-20, DEC 15 2015
abstract, full text, DOI:10.1016/j.jneuroim.2015.10.003

Kolyadko, Vladimir N.; Lushchekina, Sofya V.; Vuimo, Tatiana A.; Surov, Stepan S.; Ovsepyan, Ruzanna A.; Korneeva, Vera A.; Vorobiev, Ivan I.; Orlova, Nadezhda A.; Minakhin, Leonid; Kuznedelov, Konstantin; Severinov, Konstantin V.; Ataullakhanov, Fazoil I.; Panteleev, Mikhail A.
New Infestin-4 Mutants with Increased Selectivity against Factor XIIa
PLOS ONE, 10 Art. No. e0144940, DEC 15 2015
abstract, full text, DOI:10.1371/journal.pone.0144940

Czajkowsky, Daniel M.; Sun, Jielin; Shen, Yi; Shao, Zhifeng
Single molecule compression reveals intra-protein forces drive cytotoxin pore formation
ELIFE, 4 Art. No. e08421, DEC 10 2015
abstract, full text, DOI:10.7554/eLife.08421

Botan, Alexandru; Favela-Rosales, Fernando; Fuchs, Patrick F. J.; Javanainen, Matti; Kanduc, Matej; Kulig, Waldemar; Lamber, Antti; Loison, Claire; Lyubartsev, Alexander; Miettinen, Markus S.; Monticelli, Luca; Maatta, Jukka; Ollila, O. H. Samuli; Retegan, Marius; Rog, Tomasz; Santuz, Hubert; Tynkkynen, Joona
Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions
JOURNAL OF PHYSICAL CHEMISTRY B, 119:15075-15088, DEC 10 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b04878

Simakov, Nikolay A.; White, Joseph P.; DeLeon, Robert L.; Ghadersohi, Amin; Furlani, Thomas R.; Jones, Matthew D.; Gallo, Steven M.; Patra, Abani K.
Application kernels: HPC resources performance monitoring and variance analysis
CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE, 27:5238-5260, DEC 10 2015
abstract, full text, DOI:10.1002/cpe.3564

Koehler, Stephan; Schmid, Friederike; Settanni, Giovanni
Molecular Dynamics Simulations of the Initial Adsorption Stages of Fibrinogen on Mica and Graphite Surfaces
LANGMUIR, 31:13180-13190, DEC 8 2015
abstract, full text, DOI:10.1021/acs.langmuir.5b03371

Mori, Yoshiharu; Okumura, Hisashi
Simulated tempering based on global balance or detailed balance conditions: Suwa-Todo, heat bath, and Metropolis algorithms
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:2344-2349, DEC 5 2015
abstract, full text, DOI:10.1002/jcc.24213

Chen, Po-Han; Unger, Vinzenz; He, Xiaolin
Structure of Full-Length Human PDGFR beta Bound to Its Activating Ligand PDGF-B as Determined by Negative-Stain Electron Microscopy
JOURNAL OF MOLECULAR BIOLOGY, 427:3921-3934, DEC 4 2015
abstract, full text, DOI:10.1016/j.jmb.2015.10.003

Navarrete, Karen R.; Alderete, Joel B.; Jimenez, Veronica A.
Structural basis for drug resistance conferred by beta-tubulin mutations: a molecular modeling study on native and mutated tubulin complexes with epothilone B
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:2530-2540, DEC 2 2015
abstract, full text, DOI:10.1080/07391102.2015.1063455

Hannan, Abdul; Abraham, Neethu Maria; Goyal, Siddharth; Jamir, Imlitoshi; Priyakumar, U. Deva; Mishra, Krishnaveni
Sumoylation of Sir2 differentially regulates transcriptional silencing in yeast
NUCLEIC ACIDS RESEARCH, 43:10213-10226, DEC 2 2015
abstract, full text, DOI:10.1093/nar/gkv842

Yang, Darren; Boyer, Benjamin; Prevost, Chantal; Danilowicz, Claudia; Prentiss, Mara
Integrating multi-scale data on homologous recombination into a new recognition mechanism based on simulations of the RecA-ssDNA/dsDNA structure
NUCLEIC ACIDS RESEARCH, 43:10251-10263, DEC 2 2015
abstract, full text, DOI:10.1093/nar/gkv883

Sun, Ming; Li, Wen; Blomqvist, Karin; Das, Sanchaita; Hashem, Yaser; Dvorin, Jeffrey D.; Frank, Joachim
Dynamical features of the Plasmodium falciparum ribosome during translation
NUCLEIC ACIDS RESEARCH, 43:10515-10524, DEC 2 2015
abstract, full text, DOI:10.1093/nar/gkv991

Papaioannou, Anastasios; Kuyucak, Serdar; Kuncic, Zdenka
Molecular Dynamics Simulations of Insulin: Elucidating the Conformational Changes that Enable Its Binding
PLOS ONE, 10 Art. No. e0144058, DEC 2 2015
abstract, full text, DOI:10.1371/journal.pone.0144058

Borisova, Anna S.; Eneyskaya, Elena V.; Bobrov, Kirill S.; Jana, Suvamay; Logachev, Anton; Polev, Dmitrii E.; Lapidus, Alla L.; Ibatullin, Farid M.; Saleem, Umair; Sandgren, Mats; Payne, Christina M.; Kulminskaya, Anna A.; Stahlberg, Jerry
Sequencing, biochemical characterization, crystal structure and molecular dynamics of cellobiohydrolase Cel7A from Geotrichum candidum 3C
FEBS JOURNAL, 282:4515-4537, DEC 2015
abstract, full text, DOI:10.1111/febs.13509

Ben Imeddourene, Akli; Elbahnsi, Ahmad; Gueroult, Marc; Oguey, Christophe; Foloppe, Nicolas; Hartmann, Brigitte
Simulations Meet Experiment to Reveal New Insights into DNA Intrinsic Mechanics
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004631, DEC 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004631

Yoon, Gwonchan; Lee, Myeongsang; Kim, Kyungwoo; Kim, Jae In; Chang, Hyun Joon; Baek, Inchul; Eom, Kilho; Na, Sungsoo
Morphology and mechanical properties of multi-stranded amyloid fibrils probed by atomistic and coarse-grained simulations
PHYSICAL BIOLOGY, 12 Art. No. 066021, DEC 2015
abstract, full text, DOI:10.1088/1478-3975/12/6/066021

Wang, Lin; Li, Lin; Alexov, Emil
pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:2186-2197, DEC 2015
abstract, full text, DOI:10.1002/prot.24935

Vass, Marton; Jojart, Balazs; Bogar, Ferenc; Paragi, Gabor; Keseru, Gyoergy M.; Tarcsay, Akos
Dynamics and structural determinants of ligand recognition of the 5-HT6 receptor
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 29:1137-1149, DEC 2015
abstract, full text, DOI:10.1007/s10822-015-9883-y

Sheng, Yinghong; Zhong, Linghao; Guo, Dahai; Lau, Gavin; Feng, Changjian
Insight into structural rearrangements and interdomain interactions related to electron transfer between flavin mononucleotide and heme in nitric oxide synthase: A molecular dynamics study
JOURNAL OF INORGANIC BIOCHEMISTRY, 153:186-196, DEC 2015
abstract, full text, DOI:10.1016/j.jinorgbio.2015.08.006

Loeffler, Hannes H.; Michel, Julien; Woods, Christopher
FESetup: Automating Setup for Alchemical Free Energy Simulations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:2485-2490, DEC 2015
abstract, full text, DOI:10.1021/acs.jcim.5b00368

Bovigny, Christophe; Tamo, Giorgio; Lemmin, Thomas; Maino, Nicolas; Dal Peraro, Matteo
Lipid Builder: A Framework To Build Realistic Models for Biological Membranes
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:2491-2499, DEC 2015
abstract, full text, DOI:10.1021/acs.jcim.5b00501

Grazioso, Giovanni; Sgrignani, Jacopo; Capelli, Romina; Matera, Carlo; Dallanoce, Clelia; De Amici, Marco; Cavalli, Andrea
Allosteric Modulation of Alpha7 Nicotinic Receptors: Mechanistic Insight through Metadynamics and Essential Dynamics
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:2528-2539, DEC 2015
abstract, full text, DOI:10.1021/acs.jcim.5b00459

Ramakrishna, S.; Padhi, Siladitya; Priyakumar, U. Deva
Modeling the structure of SARS 3a transmembrane protein using a minimum unfavorable contact approach
JOURNAL OF CHEMICAL SCIENCES, 127:2159-2169, DEC 2015
abstract, full text, DOI:10.1007/s12039-015-0982-z

Comer, Jeffrey; Chen, Ran; Poblete, Horacio; Vergara-Jaque, Ariela; Riviere, Jim E.
Predicting Adsorption Affinities of Small Molecules on Carbon Nanotubes Using Molecular Dynamics Simulation
ACS NANO, 9:11761-11774, DEC 2015
abstract, full text, DOI:10.1021/acsnano.5b03592

Lapelosa, Mauro; Patapoff, Thomas W.; Zarraga, Isidro E.
Modeling of protein-anion exchange resin interaction for the human growth hormone charge variants
BIOPHYSICAL CHEMISTRY, 207:1-6, DEC 2015
abstract, full text, DOI:10.1016/j.bpc.2015.07.004

Binesh, A. R.; Kamali, R.
Molecular dynamics insights into human aquaporin 2 water channel
BIOPHYSICAL CHEMISTRY, 207:107-113, DEC 2015
abstract, full text, DOI:10.1016/j.bpc.2015.10.002

Perez-Gordones, M. C.; Serrano, M. L.; Rojas, H.; Martinez, J. C.; Uzcanga, G.; Mendoza, M.
Presence of a thapsigargin-sensitive calcium pump in Trypanosoma evansi: Immunological, physiological, molecular and structural evidences
EXPERIMENTAL PARASITOLOGY, 159:107-117, DEC 2015
abstract, full text, DOI:10.1016/j.exppara.2015.08.017

Shen, Guo-Feng; Liu, Ting-Ting; Wang, Qi; Jiang, Min; Shi, Jie-Hua
Spectroscopic and molecular docking studies of binding interaction of gefitinib, lapatinib and sunitinib with bovine serum albumin (BSA)
JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY, 153:380-390, DEC 2015
abstract, full text, DOI:10.1016/j.jphotobiol.2015.10.023

Darre, Leonardo; Domene, Carmen
Binding of Capsaicin to the TRPV1 Ion Channel
MOLECULAR PHARMACEUTICS, 12:4454-4465, DEC 2015
abstract, full text, DOI:10.1021/acs.molpharmaceut.5b00641

Das, Amit; Gerlits, Oksana; Parks, Jerry M.; Langan, Paul; Kovalevsky, Andrey; Heller, William T.
Protein Kinase A Catalytic Subunit Primed for Action: Time-Lapse Crystallography of Michaelis Complex Formation
STRUCTURE, 23:2331-2340, DEC 1 2015
abstract, full text, DOI:10.1016/j.str.2015.10.005

Zhang Zidong; Zhang Jilong; Zheng Qingchuan; Kong Chuipeng; Li Zhengqiang; Zhang Hongxing; Ma Jianzhang
Theoretical Investigation on Binding Process of Allophanate to Allophanate Hydrolase
CHEMICAL RESEARCH IN CHINESE UNIVERSITIES, 31:1023-1028, DEC 2015
abstract, full text, DOI:10.1007/s40242-015-5108-0

Kong, Ruirui; Yi, Fengshuang; Wen, Pushuai; Liu, Jianghong; Chen, Xiaoping; Ren, Jinqi; Li, Xiaofei; Shang, Yulong; Nie, Yongzhan; Wu, Kaichun; Fan, Daiming; Zhu, Li; Feng, Wei; Wu, Jane Y.
Myo9b is a key player in SLIT/ROBO-mediated lung tumor suppression
JOURNAL OF CLINICAL INVESTIGATION, 125:4407-4420, DEC 2015
abstract, full text, DOI:10.1172/JCI81673

Le, Sarah N.; Porebski, Benjamin T.; McCoey, Julia; Fodor, James; Riley, Blake; Godlewska, Marlena; Gora, Monika; Czarnocka, Barbara; Banga, J. Paul; Hoke, David E.; Kass, Itamar; Buckle, Ashley M.
Modelling of Thyroid Peroxidase Reveals Insights into Its Enzyme Function and Autoantigenicity
PLOS ONE, 10 Art. No. e0142615, DEC 1 2015
abstract, full text, DOI:10.1371/journal.pone.0142615

Pietra, Francesco
Uptake of Organohalide Pollutants, and Release of Partially Dehalogenated Products, by NpRdhA, a 'Base-Off' Cob(II)alamin-Dependent Reductive Dehalogenase from a Deep Sea Bacterium. A Molecular Dynamics Investigation
CHEMISTRY & BIODIVERSITY, 12:1945-1953, DEC 2015
abstract, full text, DOI:10.1002/cbdv.201500195

Zobnina, V. G.; Chagovets, V. V.; Boryak, O. A.; Kosevich, M. V.
A mass spectrometric study and computer modeling of noncovalent interactions of cytosine with polyethylene glycol oligomers
JOURNAL OF ANALYTICAL CHEMISTRY, 70:1533-1541, DEC 2015
abstract, full text, DOI:10.1134/S1061934815130110

Qiu, Hu; Sarathy, Aditya; Leburton, Jean-Pierre; Schulten, Klaus
Intrinsic Stepwise Translocation of Stretched ssDNA in Graphene Nanopores
NANO LETTERS, 15:8322-8330, DEC 2015
abstract, full text, TCBG publications, DOI:10.1021/acs.nanolett.5b03963

Stirnemann, Guillaume; Sterpone, Fabio
Recovering Protein Thermal Stability Using All-Atom Hamiltonian Replica-Exchange Simulations in Explicit Solvent
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:5573-5577, DEC 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00954

Dama, James F.; Hocky, Glen M.; Sun, Rui; Voth, Gregory A.
Exploring Valleys without Climbing Every Peak: More Efficient and Forgiving Metabasin Metadynamics via Robust On-the-Fly Bias Domain Restriction
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:5638-5650, DEC 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00907

Fattebert, Jean-Luc; Lau, Edmond Y.; Bennion, Brian J.; Huang, Patrick; Lightstone, Felice C.
Large-Scale First-Principles Molecular Dynamics Simulations with Electrostatic Embedding: Application to Acetylcholinesterase Catalysis
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:5688-5695, DEC 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00606

Oehme, Daniel P.; Doblin, Monika S.; Wagner, John; Bacic, Antony; Downton, Matthew T.; Gidley, Michael J.
Gaining insight into cell wall cellulose macrofibril organisation by simulating microfibril adsorption
CELLULOSE, 22:3501-3520, DEC 2015
abstract, full text, DOI:10.1007/s10570-015-0778-9

Kamthania, Mohit; Sharma, D. K.
Screening and structure-based modeling of T-cell epitopes of Nipah virus proteome: an immunoinformatic approach for designing peptide-based vaccine
3 BIOTECH, 5:877-882, DEC 2015
abstract, full text, DOI:10.1007/s13205-015-0303-8

Liu, Xin; Li, Yajuan; Wen, Liangxue; Tao, Kun; Xiao, Qing; Cao, Weixi; Huang, Zhenglan; Gao, Miao; Li, Hui; Wang, Fang; Feng, Wenli
ABL SH3 mutant inhibits BCR-ABL activity and increases imatinib sensitivity by targeting RIN1 protein in CML cell
CANCER LETTERS, 369:222-228, DEC 1 2015
abstract, full text, DOI:10.1016/j.canlet.2015.08.017

Floros, Stelios; Liakopoulou-Kyriakides, Maria; Karatasos, Kostas; Papadopoulos, Georgios E.
Detailed study of the dielectric function of a lysozyme solution studied with molecular dynamics simulations
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 44:599-611, DEC 2015
abstract, full text, DOI:10.1007/s00249-015-1052-7

Kolly, Gaelle S.; Mukherjee, Raju; Kilacskova, Emoeke; Abriata, Luciano A.; Raccaud, Mahe; Blasko, Jaroslav; Sala, Claudia; Dal Peraro, Matteo; Mikusova, Katarina; Cole, Stewart T.
GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis
JOURNAL OF BACTERIOLOGY, 197:3686-3697, DEC 2015
abstract, full text, DOI:10.1128/JB.00628-15

Jo, Sunhwan; Jiang, Wei
A generic implementation of replica exchange with solute tempering (REST2) algorithm in NAMD for complex biophysical simulations
COMPUTER PHYSICS COMMUNICATIONS, 197:304-311, DEC 2015
abstract, full text, DOI:10.1016/j.cpc.2015.08.030

Stetz, Gabrielle; Verkhivker, Gennady M.
Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins
PLOS ONE, 10 Art. No. e0143752, NOV 30 2015
abstract, full text, DOI:10.1371/journal.pone.0143752

Liang, Qiansheng; Anderson, Warren D.; Jones, Shelly T.; Souza, Caio S.; Hosoume, Juliana M.; Treptow, Werner; Covarrubias, Manuel
Positive Allosteric Modulation of Kv Channels by Sevoflurane: Insights into the Structural Basis of Inhaled Anesthetic Action
PLOS ONE, 10 Art. No. e0143363, NOV 24 2015
abstract, full text, DOI:10.1371/journal.pone.0143363

Mena-Ulecia, Karel; Tiznado, William; Caballero, Julio
Study of the Differential Activity of Thrombin Inhibitors Using Docking, QSAR, Molecular Dynamics, and MM-GBSA
PLOS ONE, 10 Art. No. e0142774, NOV 24 2015
abstract, full text, DOI:10.1371/journal.pone.0142774

Nazaruk, Ewa; Miszta, Przemyslaw; Filipek, Slawomir; Gorecka, Ewa; Landau, Ehud M.; Bilewicz, Renata
Lyotropic Cubic Phases for Drug Delivery: Diffusion and Sustained Release from the Mesophase Evaluated by Electrochemical Methods
LANGMUIR, 31:12753-12761, NOV 24 2015
abstract, full text, DOI:10.1021/acs.langmuir.5b03247

Simonov, Alexandr N.; Holien, Jessica K.; Yeung, Joyee Chun In; Nguyen, Ann D.; Corbin, C. Jo; Zheng, Jie; Kuznetsov, Vladimir L.; Auchus, Richard J.; Conley, Alan J.; Bond, Alan M.; Parker, Michael W.; Rodgers, Raymond J.; Martin, Lisandra L.
Mechanistic Scrutiny Identifies a Kinetic Role for Cytochrome b5 Regulation of Human Cytochrome P450c17 (CYP17A1, P450 17A1)
PLOS ONE, 10 Art. No. e0141252, NOV 20 2015
abstract, full text, DOI:10.1371/journal.pone.0141252

Cheng, Huaigang; Song, Huiping
Investigation of bio-removing metal ions from wastewater-a viewpoint of micro forces
DESALINATION AND WATER TREATMENT, 56:2118-2130, NOV 20 2015
abstract, full text, DOI:10.1080/19443994.2014.958764

Bravo-Rodriguez, Kenny; Klopries, Stephan; Koopmans, Kyra R. M.; Sundermann, Uschi; Yahiaoui, Samir; Arens, Julia; Kushnir, Susanna; Schulz, Frank; Sanchez-Garcia, Elsa
Substrate Flexibility of a Mutated Acyltransferase Domain and Implications for Polyketide Biosynthesis
CHEMISTRY & BIOLOGY, 22:1425-1430, NOV 19 2015
abstract, full text, DOI:10.1016/j.chembiol.2015.02.008

Sikdar, Samapan; Ghosh, Mahua; De Raychaudhury, Molly; Chakrabarti, J.
Quantum Chemical Studies on Stability and Chemical Activities in Calcium Ion Bound Calmodulin Loops
JOURNAL OF PHYSICAL CHEMISTRY B, 119:14652-14659, NOV 19 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b09713

Heidary, Nina; Utesch, Tillmann; Zerball, Maximilian; Horch, Marius; Millo, Diego; Fritsch, Johannes; Lenz, Oliver; von Klitzing, Regine; Hildebrandt, Peter; Fischer, Anna; Mroginski, Maria Andrea; Zebger, Ingo
Orientation-Controlled Electrocatalytic Efficiency of an Adsorbed Oxygen-Tolerant Hydrogenase
PLOS ONE, 10 Art. No. e0143101, NOV 18 2015
abstract, full text, DOI:10.1371/journal.pone.0143101

Monje-Galvan, Viviana; Klauda, Jeffery B.
Modeling Yeast Organelle Membranes and How Lipid Diversity Influences Bilayer Properties
BIOCHEMISTRY, 54:6852-6861, NOV 17 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00718

Qi, Yifei; Cheng, Xi; Lee, Jumin; Vermaas, Josh V.; Pogorelov, Taras V.; Tajkhorshid, Emad; Park, Soohyung; Klauda, Jeffery B.; Im, Wonpil
CHARMM-GUI HMMM Builder for Membrane Simulations with the Highly Mobile Membrane-Mimetic Model
BIOPHYSICAL JOURNAL, 109:2012-2022, NOV 17 2015
abstract, full text, DOI:10.1016/j.bpj.2015.10.008

Wu, Emilia L.; Qi, Yifei; Park, Soohyung; Mallajosyula, Sairam S.; MacKerell, Alexander D., Jr.; Klauda, Jeffery B.; Im, Wonpil
Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein
BIOPHYSICAL JOURNAL, 109:2090-2100, NOV 17 2015
abstract, full text, DOI:10.1016/j.bpj.2015.10.009

Dai, Qian; Xu, Jia-Jia; Li, Hui-Ji; Yi, Hai-Bo
Ion association characteristics in MgCl2 and CaCl2 aqueous solutions: a density functional theory and molecular dynamics investigation
MOLECULAR PHYSICS, 113:3545-3558, NOV 17 2015
abstract, full text, DOI:10.1080/00268976.2015.1039618

Mancini, Daiana T.; Sen, Kakali; Barbatti, Mario; Thiel, Walter; Ramalho, Teodorico C.
Excited-State Proton Transfer Can Tune the Color of Protein Fluorescent Markers
CHEMPHYSCHEM, 16:3444-3449, NOV 16 2015
abstract, full text, DOI:10.1002/cphc.201500744

Rodrigues Abadio, Ana Karina; Kioshima, Erika Seki; Leroux, Vincent; Martins, Natalia Florencio; Maigret, Bernard; Soares Felipe, Maria Sueli
Identification of New Antifungal Compounds Targeting Thioredoxin Reductase of Paracoccidioides Genus
PLOS ONE, 10 Art. No. e0142926, NOV 16 2015
abstract, full text, DOI:10.1371/journal.pone.0142926

Joseph, Prem Raj B.; Mosier, Philip D.; Desai, Umesh R.; Rajarathnam, Krishna
Solution NMR characterization of chemokine CXCL8/IL-8 monomer and dimer binding to glycosaminoglycans: structural plasticity mediates differential binding interactions
BIOCHEMICAL JOURNAL, 472:121-133, NOV 15 2015
abstract, full text, DOI:10.1042/BJ20150059

Wang, Jianping; Yang, Fan; Shi, Jipei; Zhao, Juan
Structural dynamics of N-ethylpropionamide clusters examined by nonlinear infrared spectroscopy
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 185102, NOV 14 2015
abstract, full text, DOI:10.1063/1.4935579

Gambini, Luca; Rizzi, Luca; Pedretti, Alessandro; Taglialatela-Scafati, Orazio; Carucci, Mario; Pancotti, Andrea; Galli, Corinna; Read, Martin; Giurisato, Emanuele; Romeo, Sergio; Russo, Ilaria
Picomolar Inhibition of Plasmepsin V, an Essential Malaria Protease, Achieved Exploiting the Prime Region
PLOS ONE, 10 Art. No. e0142509, NOV 13 2015
abstract, full text, DOI:10.1371/journal.pone.0142509

Cheng, Yuanhua; Rao, Vijay; Tu, An-yue; Lindert, Steffen; Wang, Dan; Oxenford, Lucas; McCulloch, Andrew D.; McCammon, J. Andrew; Regnier, Michael
Troponin I Mutations R146G and R21C Alter Cardiac Troponin Function, Contractile Properties, and Modulation by Protein Kinase A (PKA)-mediated Phosphorylation
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:27749-27766, NOV 13 2015
abstract, full text, DOI:10.1074/jbc.M115.683045

Meneksedag-Erol, Deniz; Bahadur, Remant K. C.; Tang, Tian; Uludag, Hasan
A Delicate Balance When Substituting a Small Hydrophobe onto Low Molecular Weight Polyethylenimine to Improve Its Nucleic Acid Delivery Efficiency
ACS APPLIED MATERIALS & INTERFACES, 7:24822-24832, NOV 11 2015
abstract, full text, DOI:10.1021/acsami.5b07929

Wang Shuangshuang; Liu Peng; Cai Wensheng; Shao Xueguang
Effect of Hydrophobicity of Threads on the Solvent-controlled Shuttling in Rotaxanes
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 36:2211-2219, NOV 10 2015
abstract, full text, DOI:10.7503/cjcu20150620

Guo, Qing; He, Yufan; Lu, Peter
Interrogating the activities of conformational deformed enzyme by single-molecule fluorescence-magnetic tweezers microscopy
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:13904-13909, NOV 10 2015
abstract, full text, DOI:10.1073/pnas.1506405112

Tadepalli, Sirimuvva; Kuang, Zhifeng; Jiang, Qisheng; Liu, Keng-Ku; Fisher, Marilee A.; Morrissey, Jeremiah J.; Kharasch, Evan D.; Slocik, Joseph M.; Naik, Rajesh R.; Singamaneni, Srikanth
Peptide Functionalized Gold Nanorods for the Sensitive Detection of a Cardiac Biomarker Using Plasmonic Paper Devices
Scientific Reports, 5 Art. No. 16206, NOV 10 2015
abstract, full text, DOI:10.1038/srep16206

Rydzewski, J.; Jakubowski, R.; Nowak, W.
Communication: Entropic measure to prevent energy over-minimization in molecular dynamics simulations
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 171103, NOV 7 2015
abstract, full text, DOI:10.1063/1.4935370

Chantreau, Vanessa; Taddese, Bruck; Munier, Mathilde; Gourdin, Louis; Henrion, Daniel; Rodien, Patrice; Chabbert, Marie
Molecular Insights into the Transmembrane Domain of the Thyrotropin Receptor
PLOS ONE, 10 Art. No. e0142250, NOV 6 2015
abstract, full text, DOI:10.1371/journal.pone.0142250

Roy, Sourav; Basu, Sankar; Dasgupta, Dipak; Bhattacharyya, Dhananjay; Banerjee, Rahul
The Unfolding MD Simulations of Cyclophilin: Analyzed by Surface Contact Networks and Their Associated Metrics
PLoS One, 10 Art. No. e0142173, NOV 6 2015
abstract, full text, DOI:10.1371/journal.pone.0142173

Xu Wei; Lan Zhong; Peng Ben-Li; Wen Rong-Fu; Ma Xue-Hu
Molecular dynamics simulation on the wetting characteristic of micro-droplet on surfaces with different free energies
ACTA PHYSICA SINICA, 64 Art. No. 216801, NOV 5 2015
abstract, full text, DOI:10.7498/aps.64.216801

Kim, Woojae; Sung, Jooyoung; Park, Kyu Hyung; Shimizu, Hideyuki; Imamura, Mika; Han, Minwoo; Sim, Eunji; Iyoda, Masahiko; Kim, Dongho
The Role of Linkers in the Excited-State Dynamic Planarization Processes of Macrocyclic Oligothiophene 12-Mers
Journal of Physical Chemistry Letters, 6:4444-4450, NOV 5 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b02189

Grosch, Jason S.; Yang, Jing; Shen, Alice; Sereda, Yuriy V.; Ortoleva, Peter J.
Broad spectrum assessment of the epitope fluctuation-Immunogenicity hypothesis
VACCINE, 33:5945-5949, NOV 4 2015
abstract, full text, DOI:10.1016/j.vaccine.2015.06.111

Wan, Rongzheng; Wang, Chunlei; Lei, Xiaoling; Zhou, Guoquan; Fang, Haiping
Enhancement of Water Evaporation on Solid Surfaces with Nanoscale Hydrophobic-Hydrophilic Patterns
PHYSICAL REVIEW LETTERS, 115 Art. No. 195901, NOV 4 2015
abstract, full text, DOI:10.1103/PhysRevLett.115.195901

Cheng, Mary Hongying; Bahar, Ivet
Molecular Mechanism of Dopamine Transport by Human Dopamine Transporter
STRUCTURE, 23:2171-2181, NOV 3 2015
abstract, full text, DOI:10.1016/j.str.2015.09.001

Li, Qufei; Shen, Rong; Treger, Jeremy S.; Wanderling, Sherry S.; Milewski, Wieslawa; Siwowska, Klaudia; Bezanilla, Francisco; Perozo, Eduardo
Resting state of the human proton channel dimer in a lipid bilayer
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E5926-E5935, NOV 3 2015
abstract, full text, DOI:10.1073/pnas.1515043112

Gaidos, Gabriel; Panaitiu, Alexandra E.; Guo, Bingqian; Pellegrini, Maria; Mierke, Dale F.
Identification and Characterization of the Interaction Site between cFLIP(L) and Calmodulin
PLOS ONE, 10 Art. No. e0141692, NOV 3 2015
abstract, full text, DOI:10.1371/journal.pone.0141692

Chen, Qi; Luan, Zheng-Jiao; Yu, Hui-Lei; Cheng, Xiaolin; Xu, Jian-He
Rational design of a carboxylic esterase RhEst1 based on computational analysis of substrate binding
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 62:319-324, NOV 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.10.015

Khakbaz, Pouyan; Klauda, Jeffery B.
Probing the importance of lipid diversity in cell membranes via molecular simulation
CHEMISTRY AND PHYSICS OF LIPIDS, 192:12-22, NOV 2015
abstract, full text, DOI:10.1016/j.chemphyslip.2015.08.003

Ballut, Lionel; Violot, Sebastien; Shivakumaraswamy, Santosh; Thota, Lakshmi Prasoona; Sathya, Manu; Kunala, Jyothirmai; Dijkstra, Bauke W.; Terreux, Raphael; Haser, Richard; Balaram, Hemalatha; Aghajari, Nushin
Active site coupling in Plasmodium falciparum GMP synthetase is triggered by domain rotation
NATURE COMMUNICATIONS, 6 Art. No. 8930, NOV 2015
abstract, full text, DOI:10.1038/ncomms9930

Khelashvili, George; Stanley, Nathaniel; Sahai, Michelle A.; Medina, Jaime; LeVine, Michael V.; Shi, Lei; De Fabritiis, Gianni; Weinstein, Harel
Spontaneous Inward Opening of the Dopamine Transporter Is Triggered by PIP2-Regulated Dynamics of the N-Terminus
ACS CHEMICAL NEUROSCIENCE, 6:1825-1837, NOV 2015
abstract, full text, DOI:10.1021/acschemneuro.5b00179

Knapp, Bernhard; Demharter, Samuel; Esmaielbeiki, Reyhaneh; Deane, Charlotte M.
Current status and future challenges in T-cell receptor/peptide/MHC molecular dynamics simulations
BRIEFINGS IN BIOINFORMATICS, 16:1035-1044, NOV 2015
abstract, full text, DOI:10.1093/bib/bbv005

Oliveira, Bruno L.; Morais, Mauricio; Mendes, Filipa; Moreira, Irina S.; Cordeiro, Carlos; Fernandes, Pedro A.; Ramos, Maria J.; Alberto, Roger; Santos, Isabel; Correia, Joao D. G.
Re(I) and Tc(I) Complexes for Targeting Nitric Oxide Synthase: Influence of the Chelator in the Affinity for the Enzyme
CHEMICAL BIOLOGY & DRUG DESIGN, 86:1072-1086, NOV 2015
abstract, full text, DOI:10.1111/cbdd.12575

Debnath, Utsab; Verma, Saroj; Singh, Pankaj; Rawat, Kavita; Gupta, Satish K.; Tripathi, Raj K.; Siddiqui, Hefazat H.; Katti, Seturam B.; Prabhakar, Yenamandra S.
Synthesis, Biological Evaluation and Molecular Modeling Studies of New 2,3-Diheteroaryl Thiazolidin-4-Ones as NNRTIs
CHEMICAL BIOLOGY & DRUG DESIGN, 86:1285-1291, NOV 2015
abstract, full text, DOI:10.1111/cbdd.12591

Pang, Chun-Li; Yuan, Hong-Bo; Cao, Tian-Guang; Su, Ji-Guo; Chen, Ya-Fei; Liu, Hui; Yu, Hui; Zhang, Hai-Ling; Zhan, Yong; An, Hai-Long; Han, Yue-Bin
Molecular simulation assisted identification of Ca2+ binding residues in TMEM16A
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 29:1035-1043, NOV 2015
abstract, full text, DOI:10.1007/s10822-015-9876-x

Santos, Lucianna Helene; Ferreira, Rafaela Salgado; Caffarena, Ernesto Raul
Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors
MEMORIAS DO INSTITUTO OSWALDO CRUZ, 110:847-864, NOV 2015
abstract, full text, DOI:10.1590/0074-02760150239

Manocheewa, Siriphan; Mittler, John E.; Samudrala, Ram; Mullins, James I.
Composite Sequence-Structure Stability Models as Screening Tools for Identifying Vulnerable Targets for HIV Drug and Vaccine Development
VIRUSES-BASEL, 7:5718-5735, NOV 2015
abstract, full text, DOI:10.3390/v7112901

Peng, Yunhui; Suryadi, Jimmy; Yang, Ye; Kucukkal, Tugba G.; Cao, Weiguo; Alexov, Emil
Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 16:27270-27287, NOV 2015
abstract, full text, DOI:10.3390/ijms161126022

Sanchez-Moreno, Israel; Bordes, Isabel; Castillo, Raquel; Javier Ruiz-Perina, Jose; Moliner, Vicent; Garcia-Junceda, Eduardo
Tuning the Phosphoryl Donor Specificity of Dihydroxyacetone Kinase from ATP to Inorganic Polyphosphate. An Insight from Computational Studies
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 16:27835-27849, NOV 2015
abstract, full text, DOI:10.3390/ijms161126073

Banerjee, Avik; Dasgupta, Subrata; Mukhopadhyay, Bishnu P.; Sekar, Kanagaraj
The putative role of some conserved water molecules in the structure and function of human transthyretin
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 71:2248-2266, NOV 2015
abstract, full text, DOI:10.1107/S1399004715016004

Galiano, Vicente; Villalain, Jose
Oleuropein aglycone in lipid bilayer membranes. A molecular dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:2849-2858, NOV 2015
abstract, full text, DOI:10.1016/j.bbamem.2015.08.007

Martin, Lisandra L.; Holien, Jessica K.; Mizrachi, Dario; Corbin, C. Jo; Conley, Alan J.; Parker, Michael W.; Rodgers, Raymond J.
Evolutionary comparisons predict that dimerization of human cytochrome P450 aromatase increases its enzymatic activity and efficiency
JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY, 154:294-301, NOV 2015
abstract, full text, DOI:10.1016/j.jsbmb.2015.09.006

Kappel, Kalli; Miao, Yinglong; McCammon, J. Andrew
Accelerated molecular dynamics simulations of ligand binding to a muscarinic G-protein-coupled receptor
QUARTERLY REVIEWS OF BIOPHYSICS, 48:479-487, NOV 2015
abstract, full text, DOI:10.1017/S0033583515000153

Belkin, Maxim; Chao, Shu-Han; Jonsson, Magnus P.; Dekker, Cees; Aksimentiev, Aleksei
Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA
ACS NANO, 9:10598-10611, NOV 2015
abstract, full text, DOI:10.1021/acsnano.5b04173

Misra, Santosh K.; Ghoshal, Goutam; Gartia, Manas R.; Wu, Zhe; De, Arun K.; Ye, Mao; Bromfield, Corinne R.; Williams, Emery M.; Singh, Kuldeep; Tangella, Krishnarao V.; Rund, Laurie; Schulten, Klaus; Schook, Lawrence B.; Ray, Partha S.; Burdette, Everette C.; Pan, Dipanjan
Trimodal Therapy: Combining Hyperthermia with Repurposed Bexarotene and Ultrasound for Treating Liver Cancer
ACS NANO, 9:10695-10718, NOV 2015
abstract, full text, TCBG publications, DOI:10.1021/acsnano.5b05974

Pietropaolo, Adriana; D'Urso, Alessandro; Purrello, Roberto; Berova, Nina
Effect of Different Z-Inducers on the Stabilization of Z Portion in BZ-DNA Sequence: Correlation Between Experimental and Simulation Data
CHIRALITY, 27:773-778, NOV 2015
abstract, full text, DOI:10.1002/chir.22502

Johnson, Matthew C.; Tatum, Kelsey B.; Lynn, Jason S.; Brewer, Tess E.; Lu, Stephen; Washburn, Brian K.; Stroupe, M. Elizabeth; Jones, Kathryn M.
Sinorhizobium meliloti Phage Phi M9 Defines a New Group of T4 Superfamily Phages with Unusual Genomic Features but a Common T=16 Capsid
JOURNAL OF VIROLOGY, 89:10945-10958, NOV 2015
abstract, full text, DOI:10.1128/JVI.01353-15

Zhou, Hao; Li, Shangyang; Badger, John; Nalivaika, Ellen; Cai, Yufeng; Foulkes-Murzycki, Jennifer; Schiffer, Celia; Makowski, Lee
Modulation of HIV protease flexibility by the T80N mutation
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1929-1939, NOV 2015
abstract, full text, DOI:10.1002/prot.24737

Ozbaykal, Gizem; Atilgan, Ali Rana; Atilgan, Canan
In silico mutational studies of Hsp70 disclose sites with distinct functional attributes
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:2077-2090, NOV 2015
abstract, full text, DOI:10.1002/prot.24925

Scherer, Martin K.; Trendelkamp-Schroer, Benjamin; Paul, Fabian; Perez-Hernandez, Guillermo; Hoffmann, Moritz; Plattner, Nuria; Wehmeyer, Christoph; Prinz, Jan-Hendrik; Noe, Frank
PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:5525-5542, NOV 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00743

Luo, Jinping; Liu, Lijun; Su, Peng; Duan, Pengbo; Lu, Daihui
A piecewise lookup table for calculating nonbonded pairwise atomic interactions
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 288, NOV 2015
abstract, full text, DOI:10.1007/s00894-015-2833-8

Ramirez-Salinas, Gema L.; Garcia-Machorro, J.; Quiliano, Miguel; Zimic, Mirko; Briz, Veronica; Rojas-Hernandez, Saul; Correa-Basurto, J.
Molecular modeling studies demonstrate key mutations that could affect the ligand recognition by influenza AH1N1 neuraminidase
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 292, NOV 2015
abstract, full text, DOI:10.1007/s00894-015-2835-6

Stanton, Richard A.; Nettles, James H.; Schinazi, Raymond F.
Ligand similarity guided receptor selection enhances docking accuracy and recall for non-nucleoside HIV reverse transcriptase inhibitors
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 282, NOV 2015
abstract, full text, DOI:10.1007/s00894-015-2826-7

Schoeler, Constantin; Bernardi, Rafael C.; Malinowska, Klara H.; Durner, Ellis; Ott, Wolfgang; Bayer, Edward A.; Schulten, Klaus; Nash, Michael A.; Gaub, Hermann E.
Mapping Mechanical Force Propagation through Biomolecular Complexes
NANO LETTERS, 15:7370-7376, NOV 2015
abstract, full text, TCBG publications, DOI:10.1021/acs.nanolett.5b02727

Stegeman, John J.; Behrendt, Lars; Woodin, Bruce R.; Kubota, Akira; Lemaire, Benjamin; Pompon, Denis; Goldstone, Jared V.; Urban, Philippe
Functional characterization of zebrafish cytochrome P450 1 family proteins expressed in yeast
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:2340-2352, NOV 2015
abstract, full text, DOI:10.1016/j.bbagen.2015.07.010

Singh, Satya P.; Foley, John F.; Zhang, Hongwei H.; Hurt, Darrell E.; Richards, Jennifer L.; Smith, Craig S.; Liao, Fang; Farber, Joshua M.
Selectivity in the Use of G(i/o) Proteins Is Determined by the DRF Motif in CXCR6 and Is Cell-Type Specific
MOLECULAR PHARMACOLOGY, 88:894-910, NOV 2015
abstract, full text, DOI:10.1124/mol.115.099960

Adams, Bryn L.; Hurley, Margaret M.; Jahnke, Justin P.; Stratis-Cullum, Dimitra N.
Functional and Selective Bacterial Interfaces Using Cross-Scaffold Gold Binding Peptides
JOM, 67:2483-2493, NOV 2015
abstract, full text, DOI:10.1007/s11837-015-1662-7

Qian, Yi; Zhang, Jie; Hu, Qinglin; Xu, Ming; Chen, Yue; Hu, Guoqing; Zhao, Meirong; Liu, Sijin
Silver nanoparticle-induced hemoglobin decrease involves alteration of histone 3 methylation status
BIOMATERIALS, 70:12-22, NOV 2015
abstract, full text, DOI:10.1016/j.biomaterials.2015.08.015

Li, Chun-Yang; Chen, Xiu-Lan; Shao, Xuan; Wei, Tian-Di; Wang, Peng; Xie, Bin-Bin; Qin, Qi-Long; Zhang, Xi-Ying; Su, Hai-Nan; Song, Xiao-Yan; Shi, Mei; Zhou, Bai-Cheng; Zhang, Yu-Zhong
Mechanistic Insight into Trimethylamine N-Oxide Recognition by the Marine Bacterium Ruegeria pomeroyi DSS-3
JOURNAL OF BACTERIOLOGY, 197:3378-3387, NOV 2015
abstract, full text, DOI:10.1128/JB.00542-15

Spiwok, Vojtech; Sucur, Zoran; Hosek, Petr
Enhanced sampling techniques in biomolecular simulations
BIOTECHNOLOGY ADVANCES, 33:1130-1140, NOV 1 2015
abstract, full text, DOI:10.1016/j.biotechadv.2014.11.011

Timucin, Ahmet Can; Bodur, Cagri; Basaga, Huveyda
SIRT1 contributes to aldose reductase expression through modulating NFAT5 under osmotic stress: In vitro and in silico insights
CELLULAR SIGNALLING, 27:2160-2172, NOV 2015
abstract, full text, DOI:10.1016/j.cellsig.2015.08.013

Ghodsi, Hossein; Darvish, Kurosh
Investigation of mechanisms of viscoelastic behavior of collagen molecule
JOURNAL OF THE MECHANICAL BEHAVIOR OF BIOMEDICAL MATERIALS, 51:194-204, NOV 2015
abstract, full text, DOI:10.1016/j.jmbbm.2015.07.015

Billesbolle, Christian B.; Kruger, Mie B.; Shi, Lei; Quick, Matthias; Li, Zheng; Stolzenberg, Sebastian; Kniazeff, Julie; Gotfryd, Kamil; Mortensen, Jonas S.; Javitch, Jonathan A.; Weinstein, Harel; Loland, Claus J.; Gether, Ulrik
Substrate-induced Unlocking of the Inner Gate Determines the Catalytic Efficiency of a Neurotransmitter:Sodium Symporter
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:26725-26738, OCT 30 2015
abstract, full text, DOI:10.1074/jbc.M115.677658

Baratto, Maria Camilla; Sinicropi, Adalgisa; Linde, Dolores; Saez-Jimenez, Veronica; Sorace, Lorenzo; Ruiz-Duenas, Francisco J.; Martinez, Angel T.; Basosi, Riccardo; Pogni, Rebecca
Redox-Active Sites in Auricularia auricula-judae Dye-Decolorizing Peroxidase and Several Directed Variants: A Multifrequency EPR Study
JOURNAL OF PHYSICAL CHEMISTRY B, 119:13583-13592, OCT 29 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b02961

Milanovsky, Georgy E.; Shuvalov, Vladimir A.; Semenov, Alexey Yu.; Cherepanov, Dmitry A.
Elastic Vibrations in the Photosynthetic Bacterial Reaction Center Coupled to the Primary Charge Separation: Implications from Molecular Dynamics Simulations and Stochastic Langevin Approach
JOURNAL OF PHYSICAL CHEMISTRY B, 119:13656-13667, OCT 29 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03036

Livada, Jovan; Martinie, Ryan J.; Dassama, Laura M. K.; Krebs, Carsten; Bollinger, J. Martin, Jr.; Silakov, Alexey
Direct Measurement of the Radical Translocation Distance in the Class I Ribonucleotide Reductase from Chlamydia trachomatis
JOURNAL OF PHYSICAL CHEMISTRY B, 119:13777-13784, OCT 29 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b04057

Shlyakhtenko, Luda S.; Dutta, Samrat; Banga, Jaspreet; Li, Ming; Harris, Reuben S.; Lyubchenko, Yuri L.
APOBEC3G Interacts with ssDNA by Two Modes: AFM Studies
SCIENTIFIC REPORTS, 5 Art. No. 15648, OCT 27 2015
abstract, full text, DOI:10.1038/srep15648

Sena, Mohan Maruthi; Morrow, Christin P.; Kirkpatrick, R. James; Krishnan, Marimuthu
Supercritical Carbon Dioxide at Smectite Mineral-Water Interfaces: Molecular Dynamics and Adaptive Biasing Force Investigation of CO2/H2O Mixtures Nanoconfined in Na-Montmorillonite
CHEMISTRY OF MATERIALS, 27:6946-6959, OCT 27 2015
abstract, full text, DOI:10.1021/acs.chemmater.5b01855

Azamat, Jafar; Sardroodi, Jaber Jahanbin; Rastkar, Alireza
Molecular dynamics simulation of ion separation and water transport through boron nitride nanotubes
DESALINATION AND WATER TREATMENT, 56:1090-1098, OCT 23 2015
abstract, full text, DOI:10.1080/19443994.2014.944571

de Veer, Simon J.; Wang, Conan K.; Harris, Jonathan M.; Craik, David J.; Swedberg, Joakim E.
Improving the Selectivity of Engineered Protease Inhibitors: Optimizing the P2 Prime Residue Using a Versatile Cyclic Peptide Library
JOURNAL OF MEDICINAL CHEMISTRY, 58:8257-8268, OCT 22 2015
abstract, full text, DOI:10.1021/acs.jmedchem.5b01148

Alberga, Domenico; Mangiatordi, Giuseppe Felice; Labat, Frederic; Ciofini, Ilaria; Nicolotti, Orazio; Lattanzi, Gianluca; Adamo, Carlo
Theoretical Investigation of Hole Transporter Materials for Energy Devices
JOURNAL OF PHYSICAL CHEMISTRY C, 119:23890-23898, OCT 22 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b08981

Adluri, Archita N. S.; Murphy, Jennifer N.; Tozer, Tiffany; Rowley, Christopher N.
Polarizable Force Field with a sigma-Hole for Liquid and Aqueous Bromomethane
JOURNAL OF PHYSICAL CHEMISTRY B, 119:13422-13432, OCT 22 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b09041

Kucukkal, Tugba G.; Yang, Ye; Uvarov, Olga; Cao, Weiguo; Alexov, Emil
Impact of Rett Syndrome Mutations on MeCP2 MBD Stability
BIOCHEMISTRY, 54:6357-6368, OCT 20 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00790

Farrugia, Mark A.; Wang, Beibei; Feig, Michael; Hausinger, Robert P.
Mutational and Computational Evidence That a Nickel-Transfer Tunnel in UreD Is Used for Activation of Klebsiella aerogenes Urease
BIOCHEMISTRY, 54:6392-6401, OCT 20 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00942

McGibbon, Robert T.; Beauchamp, Kyle A.; Harrigan, Matthew P.; Klein, Christoph; Swails, Jason M.; Hernandez, Carlos X.; Schwantes, Christian R.; Wang, Lee-Ping; Lane, Thomas J.; Pande, Vijay S.
MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
BIOPHYSICAL JOURNAL, 109:1528-1532, OCT 20 2015
abstract, full text, DOI:10.1016/j.bpj.2015.08.015

Swedberg, Joakim E.; Schroeder, Christina I.; Mitchell, Justin M.; Durek, Thomas; Fairlie, David P.; Edmonds, David J.; Griffith, David A.; Ruggeri, Roger B.; Derksen, David R.; Loria, Paula M.; Liras, Spiros; Price, David A.; Craik, David J.
Cyclic alpha-conotoxin peptidomimetic chimeras as potent GLP-1R agonists
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 103:175-184, OCT 20 2015
abstract, full text, DOI:10.1016/j.ejmech.2015.08.046

Park, Kyu Hyung; Kim, Pyosang; Kim, Woojae; Shimizu, Hideyuki; Han, Minwoo; Sim, Eunji; Iyoda, Masahiko; Kim, Dongho
Excited-State Dynamic Planarization of Cyclic Oligothiophenes in the Vicinity of a Ring-to-Linear Excitonic Behavioral Turning Point
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 54:12711-12715, OCT 19 2015
abstract, full text, DOI:10.1002/anie.201504588

Chan, Albert H.; Yi, Sung Wook; Terwilliger, Austen L.; Maresso, Anthony W.; Jung, Michael E.; Clubb, Robert T.
Structure of the Bacillus anthracis Sortase A Enzyme Bound to Its Sorting Signal A FLEXIBLE AMINO-TERMINAL APPENDAGE MODULATES SUBSTRATE ACCESS
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:25461-25474, OCT 16 2015
abstract, full text, DOI:10.1074/jbc.M115.670984

Liu, Jian; Shi, Guosheng; Guo, Pan; Yang, Jinrong; Fang, Haiping
Blockage of Water Flow in Carbon Nanotubes by Ions Due to Interactions between Cations and Aromatic Rings
PHYSICAL REVIEW LETTERS, 115 Art. No. 164502, OCT 16 2015
abstract, full text, DOI:10.1103/PhysRevLett.115.164502

Hui, Gar Kay; Wright, David W.; Vennard, Owen L.; Rayner, Lucy E.; Pang, Melisa; Yeo, See Cheng; Gor, Jayesh; Molyneux, Karen; Barratt, Jonathan; Perkins, Stephen J.
The solution structures of native and patient monomeric human IgA1 reveal asymmetric extended structures: implications for function and IgAN disease
BIOCHEMICAL JOURNAL, 471:167-185, OCT 15 2015
abstract, full text, DOI:10.1042/BJ20150612

Riley, Blake T.; Broendum, Sebastian S.; Reboul, Cyril F.; Cowieson, Nathan P.; Costa, Mauricio G. S.; Kass, Itamar; Jackson, Colin; Perahia, David; Buckle, Ashley M.; McGowan, Sheena
Dynamic Motion and Communication in the Streptococcal C1 Phage Lysin, PlyC
PLOS ONE, 10 Art. No. e0140219, OCT 15 2015
abstract, full text, DOI:10.1371/journal.pone.0140219

Pavlova, Anna; Gumbart, James C.
Parametrization of Macrolide Antibiotics Using the Force Field Toolkit
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:2052-2063, OCT 15 2015
abstract, full text, DOI:10.1002/jcc.24043

Kanchi, Subbarao; Suresh, Gorle; Priyakumar, U. Deva; Ayappa, K. G.; Maiti, Prabal K.
Molecular Dynamics Study of the Structure, Flexibility, and Hydrophilicity of PETIM Dendrimers: A Comparison with PAMAM Dendrimers
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12990-13001, OCT 15 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b07124

Konas, Ryan M.; Daristotle, John L.; Harbor, Ndubuisi B.; Klauda, Jeffery B.
Biophysical Changes of Lipid Membranes in the Presence of Ethanol at Varying Concentrations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:13134-13141, OCT 15 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b06066

MacDonald, Corey A.; Boyd, Russell J.
Competing nitrile hydratase catalytic mechanisms: Is cysteine-sulfenic acid acting as a nucleophile?
COMPUTATIONAL AND THEORETICAL CHEMISTRY, 1070:48-54, OCT 15 2015
abstract, full text, DOI:10.1016/j.comptc.2015.07.010

Schneider, Miriam; Kasanetz, Fernando; Lynch, Diane L.; Friemel, Chris M.; Lassalle, Olivier; Hurst, Dow P.; Steindel, Frauke; Monory, Krisztina; Schaefer, Carola; Miederer, Isabelle; Leweke, F. Markus; Schreckenberger, Mathias; Lutz, Beat; Reggio, Patricia H.; Manzoni, Olivier J.; Spanagel, Rainer
Enhanced Functional Activity of the Cannabinoid Type-1 Receptor Mediates Adolescent Behavior
JOURNAL OF NEUROSCIENCE, 35:13975-13988, OCT 14 2015
abstract, full text, DOI:10.1523/JNEUROSCI.1937-15.2015

Di Maio, Danilo; Chandramouli, Balasubramanian; Brancato, Giuseppe
Pathways and Barriers for Ion Translocation through the 5-HT(3)A Receptor Channel
PLOS ONE, 10 Art. No. e0140258, OCT 14 2015
abstract, full text, DOI:10.1371/journal.pone.0140258

Ercius, Peter; Alaidi, Osama; Rames, Matthew J.; Ren, Gang
Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research
ADVANCED MATERIALS, 27:5638-5663, OCT 14 2015
abstract, full text, DOI:10.1002/adma.201501015

Belaz, Sorya; Rattier, Thibault; Lafite, Pierre; Moreau, Philippe; Routier, Francoise H.; Robert-Gangneux, Florence; Gangneux, Jean-Pierre; Daniellou, Richard
Identification, biochemical characterization, and in-vivo expression of the intracellular invertase BfrA from the pathogenic parasite Leishmania major
CARBOHYDRATE RESEARCH, 415:31-38, OCT 13 2015
abstract, full text, DOI:10.1016/j.carres.2015.07.001

Iglesias-Fernandez, Javier; Darre, Leonardo; Kohlmeyer, Axel; Thomas, Robert K.; Shen, Hsin-Hui; Domene, Carmen
Surfactin at the Water/Air Interface and in Solution
LANGMUIR, 31:11097-11104, OCT 13 2015
abstract, full text, DOI:10.1021/acs.langmuir.5b02305

Medarevic, Djordje; Kachrimanis, Kyriakos; Djuric, Zorica; Ibric, Svetlana
Influence of hydrophilic polymers on the complexation of carbamazepine with hydroxypropyl-beta-cyclodextrin
EUROPEAN JOURNAL OF PHARMACEUTICAL SCIENCES, 78:273-285, OCT 12 2015
abstract, full text, DOI:10.1016/j.ejps.2015.08.001

Hernandez, Sergio; Figueroa, Daniella; Correa, Simon; Diaz, Ariel; Aguayo, Daniel; Villanueva, Rodrigo A.
Phosphorylation at the N-terminal finger subdomain of a viral RNA-dependent RNA polymerase
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 466:21-27, OCT 9 2015
abstract, full text, DOI:10.1016/j.bbrc.2015.08.082

Shakourian-Fard, Mehdi; Kamath, Ganesh; Smith, Kassiopeia; Xiong, Hui; Sankaranarayanan, Subramanian K. R. S.
Trends in Na-Ion Solvation with Alkyl-Carbonate Electrolytes for Sodium-Ion Batteries: Insights from First-Principles Calculations
JOURNAL OF PHYSICAL CHEMISTRY C, 119:22747-22759, OCT 8 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b04706

Gc, Jeevan B.; Gerstman, Bernard S.; Chapagain, Prem P.
The Role of the Interdomain Interactions on RfaH Dynamics and Conformational Transformation
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12750-12759, OCT 8 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b05681

Chakraborty, Debashree; Taly, Antoine; Sterpone, Fabio
Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12760-12770, OCT 8 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b05791

Wan, Qun; Parks, Jerry M.; Hanson, B. Leif; Fisher, Suzanne Zoe; Ostermann, Andreas; Schrader, Tobias E.; Graham, David E.; Coates, Leighton; Langan, Paul; Kovalevsky, Andrey
Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:12384-12389, OCT 6 2015
abstract, full text, DOI:10.1073/pnas.1504986112

Madsen, Jesper J.; Ohkubo, Y. Zenmei; Peters, Gunther H.; Faber, Johan H.; Tajkhorshid, Emad; Olsen, Ole H.
Membrane Interaction of the Factor VIIIa Discoidin Domains in Atomistic Detail
BIOCHEMISTRY, 54:6123-6131, OCT 6 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00417

Modi, Niraj; Ganguly, Sonalli; Barcena-Uribarri, Ivan; Benz, Roland; van den Berg, Bert; Kleinekathoefer, Ulrich
Structure, Dynamics, and Substrate Specificity of the OprO Porin from Pseudomonas aeruginosa
BIOPHYSICAL JOURNAL, 109:1429-1438, OCT 6 2015
abstract, full text, DOI:10.1016/j.bpj.2015.07.035

Alberga, Domenico; Mangiatordi, Giuseppe Felice; Motta, Alessandro; Nicolotti, Orazio; Lattanzi, Gianluca
Effects of Different Self-Assembled Mono layers on Thin-Film Morphology: A Combined DFT/MD Simulation Protocol
LANGMUIR, 31:10693-10701, OCT 6 2015
abstract, full text, DOI:10.1021/acs.langmuir.5b02761

Megow, Joerg
How Van der Waals Interactions Influence the Absorption Spectra of Pheophorbide a Complexes: A Mixed Quantum-Classical Study
CHEMPHYSCHEM, 16:3101-3107, OCT 5 2015
abstract, full text, DOI:10.1002/cphc.201500326

Kutzner, Carsten; Pall, Szilard; Fechner, Martin; Esztermann, Ansgar; de Groot, Bert L.; Grubmueller, Helmut
Best bang for your buck: GPU nodes for GROMACS biomolecular simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:1990-2008, OCT 5 2015
abstract, full text, DOI:10.1002/jcc.24030

Mendez-Luna, D.; Martinez-Archundia, M.; Maroun, Rachid C.; Ceballos-Reyes, G.; Fragoso-Vazquez, M. J.; Gonzalez-Juarez, D. E.; Correa-Basurto, J.
Deciphering the GPER/GPR30-agonist and antagonists interactions using molecular modeling studies, molecular dynamics, and docking simulations
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:2161-2172, OCT 3 2015
abstract, full text, DOI:10.1080/07391102.2014.994102

Suresh, Gorle; Priyakumar, U. Deva
Atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme
JOURNAL OF CHEMICAL SCIENCES, 127:1701-1713, OCT 2015
abstract, full text, DOI:10.1007/s12039-015-0942-7

Kheirodin, Mohsen; Pishkenari, Hossein Nejat; Moosavi, Ali; Meghdari, Ali
Study of Biomolecules Imaging Using Molecular Dynamics Simulations
NANO, 10 Art. No. 1550096, OCT 2015
abstract, full text, DOI:10.1142/S1793292015500964

Prakash, Priyanka; Sayyed-Ahmad, Abdallah; Gorfe, Alemayehu A.
pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004469, OCT 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004469

Seyler, Sean L.; Kumar, Avishek; Thorpe, M. F.; Beckstein, Oliver
Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004568, OCT 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004568

Shen, Rong; Han, Wei; Fiorin, Giacomo; Islam, Shahidul M.; Schulten, Klaus; Roux, Benoit
Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004368, OCT 2015
abstract, full text, TCBG publications, DOI:10.1371/journal.pcbi.1004368

Votapka, Lane W.; Amaro, Rommie E.
Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004381, OCT 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004381

Wahle, Manuel; Wriggers, Willy
Multi-scale Visualization of Molecular Architecture Using Real-Time Ambient Occlusion in Sculptor
PLoS Computational Biology, 11 Art. No. e1004516, OCT 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004516

Zhao, Hanchao; Palencia, Andres; Seiradake, Elena; Ghaemi, Zhaleh; Cusack, Stephen; Luthey-Schulten, Zaida; Martinis, Susan
Analysis of the Resistance Mechanism of a Benzoxaborole Inhibitor Reveals Insight into the Leucyl-tRNA Synthetase Editing Mechanism
ACS CHEMICAL BIOLOGY, 10:2277-2285, OCT 2015
abstract, full text, DOI:10.1021/acschembio.5b00291

Alcorlo, Martin; Lopez-Perrote, Andres; Delgado, Sandra; Yebenes, Hugo; Subias, Marta; Rodriguez-Gallego, Cesar; Rodriguez de Cordoba, Santiago; Llorca, Oscar
Structural insights on complement activation
FEBS JOURNAL, 282:3883-3891, OCT 2015
abstract, full text, DOI:10.1111/febs.13399

Schur, Florian K. M.; Dick, Robert A.; Hagen, Wim J. H.; Vogt, Volker M.; Briggs, John A. G.
The Structure of Immature Virus-Like Rous Sarcoma Virus Gag Particles Reveals a Structural Role for the p10 Domain in Assembly
JOURNAL OF VIROLOGY, 89:10294-10302, OCT 2015
abstract, full text, DOI:10.1128/JVI.01502-15

Kognole, Abhishek A.; Payne, Christina M.
Cello-oligomer-binding dynamics and directionality in family 4 carbohydrate-binding modules
GLYCOBIOLOGY, 25:1100-1111, OCT 2015
abstract, full text, DOI:10.1093/glycob/cwv048

Milano, Teresa; Di Salvo, Martino Luigi; Angelaccio, Sebastiana; Pascarella, Stefano
Conserved water molecules in bacterial serine hydroxymethyltransferases
PROTEIN ENGINEERING DESIGN & SELECTION, 28:415-426, OCT 2015
abstract, full text, DOI:10.1093/protein/gzv026

Wieteska, J. R.; Welche, P. R. L.; Tu, K. -M.; ElGamacy, Mohammad; Csanyi, G.; Payne, M. C.; Chaue, P. -L.
Isoflurane does not aggregate inside POPC bilayers at high pressure: Implications for pressure reversal of general anaesthesia
CHEMICAL PHYSICS LETTERS, 638:116-121, OCT 1 2015
abstract, full text, DOI:10.1016/j.cplett.2015.07.065

Spyrakis, Francesca; Benedetti, Paolo; Decherchi, Sergio; Rocchia, Walter; Cavalli, Andrea; Alcaro, Stefano; Ortuso, Francesco; Baroni, Massimo; Cruciani, Gabriele
A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:2256-2274, OCT 2015
abstract, full text, DOI:10.1021/acs.jcim.5b00169

Suliman, FakhrEldin O.; Elbashir, Abdalla A.; Schmitz, Oliver J.
Study on the separation of ofloxacin enantiomers by hydroxylpropyl-beta-cyclodextrin as a chiral selector in capillary electrophoresis: a computational approach
JOURNAL OF INCLUSION PHENOMENA AND MACROCYCLIC CHEMISTRY, 83:119-129, OCT 2015
abstract, full text, DOI:10.1007/s10847-015-0547-2

Padariya, Monikaben; Kalathiya, Umesh; Baginski, Maciej
Structural and dynamic changes adopted by EmrE, multidrug transporter protein-Studies by molecular dynamics simulation
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:2065-2074, OCT 2015
abstract, full text, DOI:10.1016/j.bbamem.2015.05.014

Chang, Kai-Ti; Anishkin, Andriy; Patwardhan, Gauri A.; Beverly, Levi J.; Siskind, Leah J.; Colombini, Marco
Ceramide channels: destabilization by Bcl-xL and role in apoptosis
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:2374-2384, OCT 2015
abstract, full text, DOI:10.1016/j.bbamem.2015.07.013

McDougle, Daniel R.; Baylon, Javier L.; Meling, Daryl D.; Kambalyal, Amogh; Grinkova, Yelena V.; Hammernik, Jared; Tajkhorshid, Emad; Das, Aditi
Incorporation of charged residues in the CYP2J2 F-G loop disrupts CYP2J2-lipid bilayer interactions
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:2460-2470, OCT 2015
abstract, full text, DOI:10.1016/j.bbamem.2015.07.015

Marcoux, Julien; Mangione, P. Patrizia; Porcari, Riccardo; Degiacomi, Matteo T.; Verona, Guglielmo; Taylor, Graham W.; Giorgetti, Sofia; Raimondi, Sara; Sanglier-Cianferani, Sarah; Benesch, Justin L. P.; Cecconi, Ciro; Naqvi, Mohsin M.; Gillmore, Julian D.; Hawkins, Philip N.; Stoppini, Monica; Robinson, Carol V.; Pepys, Mark B.; Bellotti, Vittorio
A novel mechano-enzymatic cleavage mechanism underlies transthyretin amyloidogenesis
EMBO MOLECULAR MEDICINE, 7:1337-1349, OCT 2015
abstract, full text

Allen, Stacey M.; Lim, Erin E.; Jortzik, Esther; Preuss, Janina; Chua, Hwa Huat; MacRae, James I.; Rahlfs, Stefan; Haeussler, Kristina; Downton, Matthew T.; McConville, Malcolm J.; Becker, Katja; Ralph, Stuart A.
Plasmodium falciparum glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase is a potential drug target
FEBS JOURNAL, 282:3808-3823, OCT 2015
abstract, full text, DOI:10.1111/febs.13380

Liu, Peng; Shao, Xueguang; Cai, Wensheng
Deciphering the Mechanism Involved in the Switch On/Off of Molecular Pistons
CHINESE JOURNAL OF CHEMISTRY, 33:1199-1205, OCT 2015
abstract, full text, DOI:10.1002/cjoc.201500402

Harris, Robert C.; Pettitt, B. Montgomery
Examining the Assumptions Underlying Continuum-Solvent Models
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4593-4600, OCT 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00684

Perez, Alberto; MacCallum, Justin L.; Brini, Emiliano; Simmerling, Carlos; Dill, Ken A.
Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4770-4779, OCT 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00662

Daday, Csaba; Curutchet, Caries; Sinicropi, Adalgisa; Mennucci, Benedetta; Filippi, Claudia
Chromophore-Protein Coupling beyond Nonpolarizable Models: Understanding Absorption in Green Fluorescent Protein
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4825-4839, OCT 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00650

Darre, L.; Iglesias-Fernandez, J.; Kohlmeyer, A.; Wacklin, H.; Domene, C.
Molecular Dynamics Simulations and Neutron Reflectivity as an Effective Approach To Characterize Biological Membranes and Related Macromolecular Assemblies
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4875-4884, OCT 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00635

Choi, Hwanho; Kang, Hongsuk; Park, Hwangseo
Computational Prediction of Molecular Hydration Entropy with Hybrid Scaled Particle Theory and Free-Energy Perturbation Method
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4933-4942, OCT 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00325

Ngo, Van; da Silva, Mauricio C.; Kubillus, Maximilian; Li, Hui; Roux, Benoit; Elstner, Marcus; Cui, Qiang; Salahub, Dennis R.; Noskov, Sergei Yu.
Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4992-5001, OCT 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00524

Paz, S. Alexis; Abrams, Cameron F.
Free Energy and Hidden Barriers of the beta-Sheet Structure of Prion Protein
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:5024-5034, OCT 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00576

Qin, Xin; Xia, Wenjie; Sinko, Robert; Keten, Sinan
Tuning Glass Transition in Polymer Nanocomposites with Functionalized Cellulose Nanocrystals through Nanoconfinement
NANO LETTERS, 15:6738-6744, OCT 2015
abstract, full text, DOI:10.1021/acs.nanolett.5b02588

Fichou, Yann; Heyden, Matthias; Zaccai, Giuseppe; Weik, Martin; Tobias, Douglas J.
Molecular Dynamics Simulations of a Powder Model of the Intrinsically Disordered Protein Tau
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12580-12589, OCT 1 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b05849

Chen, Houyang; Ruckenstein, Eli
Hydrated Ions: From Individual Ions to Ion Pairs to Ion Clusters
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12671-12676, OCT 1 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b06837

Caddeo, Claudia; Cazia, Vasco; Bagolini, Luigi; Lusk, Mark T.; Mattoni, Alessandro
Pinpointing the Cause of Platinum Tipping on CdS Nanorods
JOURNAL OF PHYSICAL CHEMISTRY C, 119:22663-22668, OCT 1 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b06264

Cannon, Daniel A.; Aslikenasy, Nurit; Tuttle, Tell
Influence of Solvent in Controlling Peptide-Surface Interactions
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:3944-3949, OCT 1 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b01733

Zhang, Jiong; Barz, Bogdan; Zhang, Jingfen; Xu, Dong; Kosztin, Ioan
Selective refinement and selection of near-native models in protein structure prediction
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1823-1835, OCT 2015
abstract, full text, DOI:10.1002/prot.24866

Qu, Tao; Verma, Devendra; Alucozai, Milad; Tomar, Vikas
Influence of interfacial interactions on deformation mechanism and interface viscosity in alpha-chitin-calcite interfaces
ACTA BIOMATERIALIA, 25:325-338, OCT 1 2015
abstract, full text, DOI:10.1016/j.actbio.2015.06.034

Valenzuela-Riffo, Felipe; Tapia, Gerardo; Parra-Palma, Carolina; Morales-Quintana, Luis
Understanding the roles of Lys33 and Arg45 in the binding-site stability of LjLTP10, an LTP related to drought stress in Lotus japonicus
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 270, OCT 2015
abstract, full text, DOI:10.1007/s00894-015-2807-x

Pradhan, Shashindra M.; Katti, Kalpana S.; Katti, Dinesh R.
Evolution of Molecular Interactions in the Interlayer of Na-Montmorillonite Swelling Clay with Increasing Hydration
INTERNATIONAL JOURNAL OF GEOMECHANICS, 15 Art. No. 04014073, OCT 2015
abstract, full text, DOI:10.1061/(ASCE)GM.1943-5622.0000412

Sawada, Yasuyuki; Sokabe, Masahiro
Molecular dynamics study on protein-water interplay in the mechanogating of the bacterial mechanosensitive channel MscL
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 44:531-543, OCT 2015
abstract, full text, DOI:10.1007/s00249-015-1065-2

Chang, Shan; He, Hong-Qiu; Shen, Lin; Wan, Hua
Understanding peptide competitive inhibition of botulinum neurotoxin a binding to SV2 protein via molecular dynamics simulations
BIOPOLYMERS, 103:597-608, OCT 2015
abstract, full text, DOI:10.1002/bip.22682

van Erp, Paul B. G.; Jackson, Ryan N.; Carter, Joshua; Golden, Sarah M.; Bailey, Scott; Wiedenheft, Blake
Mechanism of CRISPR-RNA guided recognition of DNA targets in Escherichia coli
NUCLEIC ACIDS RESEARCH, 43:8381-8391, SEP 30 2015
abstract, full text, DOI:10.1093/nar/gkv793

Gorska, Anna; Jasinski, Maciej; Trylska, Joanna
MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids
NUCLEIC ACIDS RESEARCH, 43 Art. No. e114, SEP 30 2015
abstract, full text, DOI:10.1093/nar/gkv559

Westergard, Thomas; Salari, Reza; Martin, Joseph V.; Brannigan, Grace
Interactions of L-3,5,4 '-Triiodothyronine, Allopregnanolone, and Ivermectin with the GABA(A) Receptor: Evidence for Overlapping Intersubunit Binding Modes
PLOS ONE, 10 Art. No. e0139072, SEP 30 2015
abstract, full text, DOI:10.1371/journal.pone.0139072

Zisis, Themistoklis; Freddolino, Peter L.; Turunen, Petri; van Teeseing, Muriel C. F.; Rowan, Alan E.; Blank, Kerstin G.
Interfacial Activation of Candida antarctica Lipase B: Combined Evidence from Experiment and Simulation
BIOCHEMISTRY, 54:5969-5979, SEP 29 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00586

Davare, Monika A.; Vellore, Nadeem A.; Wagner, Jacob P.; Eide, Christopher A.; Goodman, James R.; Drilon, Alexander; Deininger, Michael W.; O'Hare, Thomas; Druker, Brian J.
Structural insight into selectivity and resistance profiles of ROS1 tyrosine kinase inhibitors
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E5381-E5390, SEP 29 2015
abstract, full text, DOI:10.1073/pnas.1515281112

Liu, Fei; Zhao, Yi-Lei; Wang, Xiaolei; Hu, Hongbo; Peng, Huasong; Wang, Wei; Wang, Jing-Fang; Zhang, Xuehong
y Elucidation of Enzymatic Mechanism of Phenazine Biosynthetic Protein PhzF Using QM/MM and MD Simulations
PLOS ONE, 10 Art. No. e0139081, SEP 28 2015
abstract, full text, DOI:10.1371/journal.pone.0139081

He, Xiaoxia; Shen, Yan; Hung, Francisco R.; Santiso, Erik E.
Molecular simulation of homogeneous nucleation of crystals of an ionic liquid from the melt
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 124506, SEP 28 2015
abstract, full text, DOI:10.1063/1.4931654

La Penna, G.; Minicozzi, V.; Morante, S.; Rossi, G. C.; Stellato, F.
A first-principle calculation of the XANES spectrum of Cu2+ in water
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 124508, SEP 28 2015
abstract, full text, DOI:10.1063/1.4931808

Rydzewski, J.; Nowak, W.
Memetic algorithms for ligand expulsion from protein cavities
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 124101, SEP 28 2015
abstract, full text, DOI:10.1063/1.4931181

Karim, Christine B.; Espinoza-Fonseca, L. Michel; James, Zachary M.; Hanse, Eric A.; Gaynes, Jeffrey S.; Thomas, David D.; Kelekar, Ameeta
Structural Mechanism for Regulation of Bcl-2 protein Noxa by phosphorylation
SCIENTIFIC REPORTS, 5 Art. No. 14557, SEP 28 2015
abstract, full text, DOI:10.1038/srep14557

Tanaka, Naoto; Dutrow, Emily V.; Miyadera, Keiko; Delemotte, Lucie; MacDermaid, Christopher M.; Reinstein, Shelby L.; Crumley, William R.; Dixon, Christopher J.; Casal, Margret L.; Klein, Michael L.; Aguirre, Gustavo D.; Tanaka, Jacqueline C.; Guziewicz, Karina E.
Canine CNGA3 Gene Mutations Provide Novel Insights into Human Achromatopsia-Associated Channelopathies and Treatment
PLOS ONE, 10 Art. No. e0138943, SEP 25 2015
abstract, full text, DOI:10.1371/journal.pone.0138943

Bockus, Andrew T.; Schwochert, Joshua A.; Pye, Cameron R.; Townsend, Chad E.; Sok, Vong; Bednarek, Maria A.; Lokey, R. Scott
Going Out on a Limb: Delineating The Effects of beta-Branching, N-Methylation, and Side Chain Size on the Passive Permeability, Solubility, and Flexibility of Sanguinamide A Analogues
JOURNAL OF MEDICINAL CHEMISTRY, 58:7409-7418, SEP 24 2015
abstract, full text, DOI:10.1021/acs.jmedchem.5b00919

Meher, Biswa Ranjan; Dixit, Anshuman; Bousfield, George R.; Lushington, Gerald H.
Glycosylation Effects on FSH-FSHR Interaction Dynamics: A Case Study of Different FSH Glycoforms by Molecular Dynamics Simulations
PLOS ONE, 10 Art. No. e0137897, SEP 24 2015
abstract, full text, DOI:10.1371/journal.pone.0137897

Kanaan, Natalia; Crehuet, Ramon; Imhof, Petra
Mechanism of the Glycosidic Bond Cleavage of Mismatched Thymine in Human Thymine DNA Glycosylase Revealed by Classical Molecular Dynamics and Quantum Mechanical/Molecular Mechanical Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12365-12380, SEP 24 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b05496

Chon, Nara Lee; Osterberg, J. Ryan; Henderson, Jack; Khan, Hanif M.; Reuter, Nathalie; Knight, Jefferson D.; Lin, Hai
Membrane Docking of the Synaptotagmin 7 C2A Domain: Computation Reveals Interplay between Electrostatic and Hydrophobic Contributions
BIOCHEMISTRY, 54:5696-5711, SEP 22 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00422

Gamiz-Hernandez, Ana P.; Angelova, Iva Neycheva; Send, Robert; Sundholm, Dage; Kaila, Ville R. I.
Protein-Induced Color Shift of Carotenoids in beta-Crustacyanin
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 54:11564-11566, SEP 21 2015
abstract, full text, DOI:10.1002/anie.201501609

Chatterjee, Abhijit; Bhattacharya, Swati
Uncertainty in a Markov state model with missing states and rates: Application to a room temperature kinetic model obtained using high temperature molecular dynamics
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 114109, SEP 21 2015
abstract, full text, DOI:10.1063/1.4930976

Larsen, Aaron T.; Fahrenbach, Albert C.; Sheng, Jia; Pian, Julia; Szostak, Jack W.
Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization
NUCLEIC ACIDS RESEARCH, 43:7675-7687, SEP 18 2015
abstract, full text, DOI:10.1093/nar/gkv761

Marquez-Miranda, Valeria; Belen Camarada, Maria; Araya-Duran, Ingrid; Varas-Concha, Ignacio; Eduardo Almonacid, Daniel; Danilo Gonzalez-Nilo, Fernando
Biomimetics: From Bioinformatics to Rational Design of Dendrimers as Gene Carriers
PLOS ONE, 10 Art. No. e0138392, SEP 18 2015
abstract, full text, DOI:10.1371/journal.pone.0138392

Lorch, Sebastian; Capponi, Sara; Pieront, Florian; Bondar, Ana-Nicoleta
Dynamic Carboxylate/Water Networks on the Surface of the PsbO Subunit of Photosystem II
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12172-12181, SEP 17 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b06594

Lammi, Carmen; Zanoni, Chiara; Arnoldi, Anna; Vistoli, Giulio
Two Peptides from Soy beta-Conglycinin Induce a Hypocholesterolemic Effect in HepG2 Cells by a Statin-Like Mechanism: Comparative in Vitro and in Silico Modeling Studies
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 63:7945-7951, SEP 16 2015
abstract, full text, DOI:10.1021/acs.jafc.5b03497

Kim, Steve S.; Kuang, Zhifeng; Ngo, Yen H.; Farmer, Barry L.; Naik, Rajesh R.
Biotic-Abiotic Interactions: Factors that Influence Peptide-Graphene Interactions
ACS APPLIED MATERIALS & INTERFACES, 7:20447-20453, SEP 16 2015
abstract, full text, DOI:10.1021/acsami.5b06434

Imbrici, P.; Maggi, L.; Mangiatordi, G. F.; Dinardo, M. M.; Altamura, C.; Brugnoni, R.; Alberga, D.; Pinter, G. Lauria; Ricci, G.; Siciliano, G.; Micheli, R.; Annicchiarico, G.; Lattanzi, G.; Nicolotti, O.; Morandi, L.; Bernasconi, P.; Desaphy, J. -F.; Mantegazza, R.; Camerino, D. Conte
ClC-1 mutations in myotonia congenita patients: insights into molecular gating mechanisms and genotype-phenotype correlation
JOURNAL OF PHYSIOLOGY-LONDON, 593:4181-4199, SEP 15 2015
abstract, full text, DOI:10.1113/JP270358

Ribeiro, Andre A. S. T.; Ortiz, Vanessa
MDN: A Web Portal for Network Analysis of Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 109:1110-1116, SEP 15 2015
abstract, full text, DOI:10.1016/j.bpj.2015.06.013

Earnest, Tyler M.; Lai, Jonathan; Chen, Ke; Hallock, Michael J.; Williamson, James R.; Luthey-Schulten, Zaida
Toward a Whole-Cell Model of Ribosome Biogenesis: Kinetic Modeling of SSU Assembly
BIOPHYSICAL JOURNAL, 109:1117-1135, SEP 15 2015
abstract, full text, DOI:10.1016/j.bpj.2015.07.030

Salmas, Ramin Ekhteiari; Mestanoglu, Mert; Yurtsever, Mine; Noskov, Sergei Y.; Durdagi, Serdar
Molecular Simulations of Solved Co-crystallized X-Ray Structures Identify Action Mechanisms of PDE delta Inhibitors
BIOPHYSICAL JOURNAL, 109:1163-1168, SEP 15 2015
abstract, full text, DOI:10.1016/j.bpj.2015.08.001

Floquet, Nicolas; Costa, Mauricio G. S.; Batista, Paulo R.; Renault, Pedro; Bisch, Paulo M.; Raussin, Florent; Martinez, Jean; Morris, May C.; Perahia, David
Conformational Equilibrium of CDK/Cyclin Complexes by Molecular Dynamics with Excited Normal Modes
BIOPHYSICAL JOURNAL, 109:1179-1189, SEP 15 2015
abstract, full text, DOI:10.1016/j.bpj.2015.07.003

Sumbul, Fidan; Acuner-Ozbabacan, Saliha Ece; Haliloglu, Turkan
Allosteric Dynamic Control of Binding
BIOPHYSICAL JOURNAL, 109:1190-1201, SEP 15 2015
abstract, full text, DOI:10.1016/j.bpj.2015.08.011

Sharma, Vivek; Belevich, Galina; Gamiz-Hernandez, Ana P.; Rog, Tomasz; Vattulainen, Ilpo; Verkhovskaya, Marina L.; Wikstrom, Marten; Hummer, Gerhard; Kaila, Ville R. I.
Redox-induced activation of the proton pump in the respiratory complex I
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:11571-11576, SEP 15 2015
abstract, full text, DOI:10.1073/pnas.1503761112

Koldso, Heidi; Andersen, Ole Juul; Nikolajsen, Camilla Lund; Scavenius, Carsten; Sorensen, Charlotte S.; Underhaug, Jarl; Runager, Kasper; Nielsen, Niels Chr.; Enghild, Jan J.; Schiott, Birgit
Early Events in the Amyloid Formation of the A546T Mutant of Transforming Growth Factor beta-Induced Protein in Corneal Dystrophies Compared to the Nonfibrillating R555W and R555Q Mutants
BIOCHEMISTRY, 54:5546-5556, SEP 15 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00473

Nakano, Shogo; Okazaki, Seiji; Ishitsubo, Erika; Kawahara, Nobuhiro; Komeda, Hidenobu; Tokiwa, Hiroaki; Asano, Yasuhisa
Structural and computational analysis of peptide recognition mechanism of class-C type penicillin binding protein, alkaline D-peptidase from Bacillus cereus DF4-B
SCIENTIFIC REPORTS, 5 Art. No. 13836, SEP 15 2015
abstract, full text, DOI:10.1038/srep13836

Chinappi, Mauro; Luchian, Tudor; Cecconi, Fabio
Nanopore tweezers: Voltage-controlled trapping and releasing of analytes
PHYSICAL REVIEW E, 92 Art. No. 032714, SEP 15 2015
abstract, full text, DOI:10.1103/PhysRevE.92.032714

Piazzetta, Paolo; Marino, Tiziana; Russo, Nino
Theoretical investigation on the restoring step of the carbonic anhydrase catalytic cycle for natural and promiscuous substrates
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 582:101-106, SEP 15 2015
abstract, full text, DOI:10.1016/j.abb.2015.03.022

Zuo, Zhicheng; Wang, Beibei; Weng, Jingwei; Wang, Wenning
Stepwise substrate translocation mechanism revealed by free energy calculations of doxorubicin in the multidrug transporter AcrB
SCIENTIFIC REPORTS, 5 Art. No. 13905, SEP 14 2015
abstract, full text, DOI:10.1038/srep13905

Sokhan, V. P.; Jones, A.; Cipcigan, F. S.; Crain, J.; Martyna, G. J.
Molecular-Scale Remnants of the Liquid-Gas Transition in Supercritical Polar Fluids
PHYSICAL REVIEW LETTERS, 115 Art. No. 117801, SEP 11 2015
abstract, full text, DOI:10.1103/PhysRevLett.115.117801

Poma, Adolfo B.; Chwastyk, Mateusz; Cieplak, Marek
Polysaccharide-Protein Complexes in a Coarse-Grained Model
JOURNAL OF PHYSICAL CHEMISTRY B, 119:12028-12041, SEP 10 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b06141

Lin, Wayne; Insley, Thomas; Tuttle, Marcus D.; Zhu, Lingyang; Berthold, Deborah A.; Kral, Petr; Rienstra, Chad M.; Murphy, Catherine J.
Control of Protein Orientation on Gold Nanoparticles
JOURNAL OF PHYSICAL CHEMISTRY C, 119:21035-21043, SEP 10 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b07701

Chen, Qiang; Kinde, Monica N.; Arjunan, Palaniappa; Wells, Marta M.; Cohen, Aina E.; Xu, Yan; Tang, Pei
Direct Pore Binding as a Mechanism for Isoflurane Inhibition of the Pentameric Ligand-gated Ion Channel ELIC
SCIENTIFIC REPORTS, 5 Art. No. 13833, SEP 8 2015
abstract, full text, DOI:10.1038/srep13833

Viciano, Ignacio; Castillo, Raquel; Marti, Sergio
QM/MM modeling of the hydroxylation of the androstenedione substrate catalyzed by cytochrome P450 aromatase (CYP19A1)
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:1736-1747, SEP 5 2015
abstract, full text, DOI:10.1002/jcc.23967

Zheng, Lijun; Farrell, David M.; Fulton, Ruth M.; Bagg, Eve E.; Salcedo, Ernesto; Manino, Meridee; Britt, Steven G.
Analysis of Conserved Glutamate and Aspartate Residues in Drosophila Rhodopsin 1 and Their Influence on Spectral Tuning
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:21951-21961, SEP 4 2015
abstract, full text, DOI:10.1074/jbc.M115.677765

Wang, Xinlei; Vukovic, Lela; Koh, Hye Ran; Schulten, Klaus; Myong, Sua
Dynamic profiling of double-stranded RNA binding proteins
NUCLEIC ACIDS RESEARCH, 43:7566-7576, SEP 3 2015
abstract, full text, TCBG publications, DOI:10.1093/nar/gkv726

Markegard, Cade B.; Mazaheripour, Arnir; Jocson, Jonah-Micah; Burke, Anthony M.; Dickson, Mary N.; Gorodetsky, Alon A.; Nguyen, Hung D.
Molecular Dynamics Simulations of Perylenediimide DNA Base Surrogates
JOURNAL OF PHYSICAL CHEMISTRY B, 119:11459-11465, SEP 3 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03874

Gleed, Mitchell L.; Ioannidis, Harris; Kolocouris, Antonios; Busath, David D.
Resistance-Mutation (N31) Effects on Drug Orientation and Channel Hydration in Amantadine-Bound Influenza A M2
JOURNAL OF PHYSICAL CHEMISTRY B, 119:11548-11559, SEP 3 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b05808

Parikh, Niyati D.; Klimov, Dmitri K.
Molecular Mechanisms of Alzheimer's Biomarker FDDNP Binding to A beta Amyloid Fibril
JOURNAL OF PHYSICAL CHEMISTRY B, 119:11568-11580, SEP 3 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b06112

Thibault, J. C.; Roe, D. R.; Eilbeck, K.; Cheatham, T. E., I.I.I.; Facelli, J. C.
Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology
SAR AND QSAR IN ENVIRONMENTAL RESEARCH, 26:577-593, SEP 2 2015
abstract, full text, DOI:10.1080/1062936X.2015.1076515

Saxena, A. K.; Devillers, J.; Bhunia, S. S.; Bro, E.
Modelling inhibition of avian aromatase by azole pesticides
SAR AND QSAR IN ENVIRONMENTAL RESEARCH, 26:757-782, SEP 2 2015
abstract, full text, DOI:10.1080/1062936X.2015.1090749

Hylton, Rebecca K.; Tizzard, Graham J.; Threlfall, Terence L.; Ellis, Amy L.; Coles, Simon J.; Seaton, Colin C.; Schulze, Eric; Lorenz, Heike; Seidel-Morgenstern, Andreas; Stein, Matthias; Price, Sarah L.
Are the Crystal Structures of Enantiopure and Racemic Mandelic Acids Determined by Kinetics or Thermodynamics?
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:11095-11104, SEP 2 2015
abstract, full text, DOI:10.1021/jacs.5b05938

Campomanes, Pablo; Rothlisberger, Ursula; Alfonso-Prieto, Mercedes; Rovira, Carme
The Molecular Mechanism of the Catalase-like Activity in Horseradish Peroxidase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:11170-11178, SEP 2 2015
abstract, full text, DOI:10.1021/jacs.5b06796

Noto, Rosina; Randazzo, Loredana; Raccosta, Samuele; Caccia, Sonia; Moriconi, Claudia; Miranda, Elena; Martorana, Vincenzo; Manno, Mauro
The stability and activity of human neuroserpin are modulated by a salt bridge that stabilises the reactive centre loop
SCIENTIFIC REPORTS, 5 Art. No. 13666, SEP 2 2015
abstract, full text, DOI:10.1038/srep13666

Tarus, Bogdan; Bertrand, Helene; Zedda, Gloria; Di Primo, Carmelo; Quideau, Stephane; Slama-Schwok, Anny
Structure-based design of novel naproxen derivatives targeting monomeric nucleoprotein of Influenza A virus
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:1899-1912, SEP 2 2015
abstract, full text, DOI:10.1080/07391102.2014.979230

Wang, Fangfang; Yang, Wei; Shi, Yonghui; Le, Guowei
3D-QSAR, molecular docking and molecular dynamics studies of a series of ROR gamma t inhibitors
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:1929-1940, SEP 2 2015
abstract, full text, DOI:10.1080/07391102.2014.980321

Banerjee, Avik; Mukhopadhyay, Bishnu P.
An insight to the conserved water mediated dynamics of catalytic His88 and its recognition to thyroxin and RBP binding residues in human transthyretin
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:1973-1988, SEP 2 2015
abstract, full text, DOI:10.1080/07391102.2014.984632

Moradi, Mahmoud; Enkavi, Giray; Tajkhorshid, Emad
Atomic-level characterization of transport cycle thermodynamics in the glycerol-3-phosphate: phosphate antiporter
NATURE COMMUNICATIONS, 6 Art. No. 8393, SEP 2015
abstract, full text, DOI:10.1038/ncomms9393

Uporov, Igor V.; Forlemu, Neville Y.; Nori, Rahul; Aleksandrov, Tsvetan; Sango, Boris A.; Mbote, Yvonne E. Bongfen; Pothuganti, Sandeep; Thomasson, Kathryn A.
Introducing DInaMo: A Package for Calculating Protein Circular Dichroism Using Classical Electromagnetic Theory
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 16:21237-21276, SEP 2015
abstract, full text, DOI:10.3390/ijms160921237

Hu, Dong; Gur, Mert; Zhou, Zhuan; Gamper, Armin; Hung, Mien-Chie; Fujita, Naoya; Lan, Li; Bahar, Ivet; Wan, Yong
Interplay between arginine methylation and ubiquitylation regulates KLF4-mediated genome stability and carcinogenesis
NATURE COMMUNICATIONS, 6 Art. No. 8419, SEP 2015
abstract, full text, DOI:10.1038/ncomms9419

Echeverria, Ignacia; Liu, Yunlong; Gabelli, Sandra B.; Amzel, L. Mario
Oncogenic mutations weaken the interactions that stabilize the p110 alpha-p85 alpha heterodimer in phosphatidylinositol 3-kinase alpha
FEBS JOURNAL, 282:3528-3542, SEP 2015
abstract, full text, DOI:10.1111/febs.13365

Koehler, Stephan; Schmid, Friederike; Settanni, Giovanni
The Internal Dynamics of Fibrinogen and Its Implications for Coagulation and Adsorption
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004346, SEP 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004346

Azamat, Jafar; Sattary, Batoul Shirforush; Khataee, Alireza; Joo, Sang Woo
Removal of a hazardous heavy metal from aqueous solution using functionalized graphene and boron nitride nanosheets: Insights from simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 61:13-20, SEP 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.06.012

Suresh, Gorle; Priyakumar, U. Deva
Inclusion of methoxy groups inverts the thermodynamic stabilities of DNA-RNA hybrid duplexes: A molecular dynamics simulation study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 61:150-159, SEP 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.07.009

Macalino, Stephani Joy Y.; Gosu, Vijayakumar; Hong, Sunhye; Choi, Sun
Role of computer-aided drug design in modern drug discovery
ARCHIVES OF PHARMACAL RESEARCH, 38:1686-1701, SEP 2015
abstract, full text, DOI:10.1007/s12272-015-0640-5

Mendes, Celso L.; Bode, Brett; Bauer, Gregory H.; Enos, Jeremy; Beldica, Cristina; Kramer, William T.
Deployment and testing of the sustained petascale Blue Waters system
JOURNAL OF COMPUTATIONAL SCIENCE, 10:327-337, SEP 2015
abstract, full text, DOI:10.1016/j.jocs.2015.03.007

Liu, Xiaorong; Beugelsdijk, Alex; Chen, Jianhan
Dynamics of the BH3-Only Protein Binding Interface of Bcl-xL
BIOPHYSICAL JOURNAL, 109:1049-1057, SEP 1 2015
abstract, full text, DOI:10.1016/j.bpj.2015.07.043

Carswell, Casey L.; Henault, Camille M.; Murlidaran, Sruthi; Therien, J. P. Daniel; Juranka, Peter F.; Surujballi, Julian A.; Brannigan, Grace; Baenziger, John E.
Role of the Fourth Transmembrane alpha Helix in the Allosteric Modulation of Pentameric Ligand-Gated Ion Channels
STRUCTURE, 23:1655-1664, SEP 1 2015
abstract, full text, DOI:10.1016/j.str.2015.06.020

Shadrina, Maria S.; Peslherbe, Gilles H.; English, Ann M.
Quaternary-Linked Changes in Structure and Dynamics That Modulate O-2 Migration within Hemoglobin's Gas Diffusion Tunnels
BIOCHEMISTRY, 54:5268-5278, SEP 1 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00368

Shadrina, Maria S.; Peslherbe, Gilles H.; English, Ann M.
O-2 and Water Migration Pathways between the Solvent and Heme Pockets of Hemoglobin with Open and Closed Conformations of the Distal HisE7
BIOCHEMISTRY, 54:5279-5289, SEP 1 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00369

Iacovelli, Federico; Falconi, Mattia
Decoding the conformation-linked functional properties of nucleic acids by the use of computational tools
FEBS JOURNAL, 282:3298-3310, SEP 2015
abstract, full text, DOI:10.1111/febs.13315

Sun, Dawei; Flock, Tilman; Deupi, Xavier; Maeda, Shoji; Matkovic, Milos; Mendieta, Sandro; Mayer, Daniel; Dawson, Roger J. P.; Schertler, Gebhard F. X.; Babu, M. Madan; Veprintsev, Dmitry B.
Probing G alpha(i1) protein activation at single-amino acid resolution
NATURE STRUCTURAL & MOLECULAR BIOLOGY, 22:686-U64, SEP 2015
abstract, full text, DOI:10.1038/nsmb.3070

Tan, Bowen; Zhou, Yijie; Song, Zhilei; Peng, Yinxuan; Wu, Fang; Kang, Yue; Liu, Xiaomin; Zeng, Li; Huang, Tingting; Liu, Zongying; Xiong, Lili; Guo, Zhiyun; Cui, Jian; Mao, Canquan
Modeling and Virtual Screening of Antisense Peptides Targeting the Divergent Region of Tumor-Associated MT1-MMP Protein
BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 36:2198-2207, SEP 2015
abstract, full text, DOI:10.1002/bkcs.10421

Rodriguez, Roberto A.; Yu, Lili; Chen, Liao Y.
Computing Protein-Protein Association Affinity with Hybrid Steered Molecular Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4427-4438, SEP 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00340

Savelyev, Alexey; MacKerell, Alexander D., Jr.
Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li+, Na+, K+, and Rb+ via Water-Mediated Hydrogen Bonding
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4473-4485, SEP 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00508

Qi, Yifei; Ingolfsson, Helgi I.; Cheng, Xi; Lee, Jumin; Marrink, Siewert J.; Im, Wonpil
CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4486-4494, SEP 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00513

Yang, Jing; Calero, Carles; Bonomi, Massimiliano; Marti, Jordi
Specific Ion Binding at Phospholipid Membrane Surfaces
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4495-4499, SEP 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00540

Lockhart, Christopher; O'Connor, James; Armentrout, Steven; Klimov, Dmitri K.
Greedy replica exchange algorithm for heterogeneous computing grids
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 243, SEP 2015
abstract, full text, DOI:10.1007/s00894-015-2763-5

Sung, Shen-Shu
Peptide folding driven by Van der Waals interactions
PROTEIN SCIENCE, 24:1383-1388, SEP 2015
abstract, full text, DOI:10.1002/pro.2710

Hamed, Elham; Ma, Dan; Keten, Sinan
Effect of Polymer Conjugation Site on Stability and Self-Assembly of Coiled Coils
BIONANOSCIENCE, 5:140-149, SEP 2015
abstract, full text, DOI:10.1007/s12668-015-0172-y

Ramya, L.; Gautham, N.; Chaloin, Laurent; Kajava, Andrey V.
Restricted mobility of side chains on concave surfaces of solenoid proteins may impart heightened potential for intermolecular interactions
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1654-1664, SEP 2015
abstract, full text, DOI:10.1002/prot.24851

Katti, Dinesh R.; Srinivasamurthy, Lakshmikanth; Katti, Kalpana S.
Molecular modeling of initiation of interlayer swelling in Na-montmorillonite expansive clay
CANADIAN GEOTECHNICAL JOURNAL, 52:1385-1395, SEP 2015
abstract, full text, DOI:10.1139/cgj-2014-0309

Parasuraman, Ponnusamy; Murugan, Veeramani; Selvin, Jeyasigamani F. A.; Gromiha, M. Michael; Fukui, Kazuhiko; Veluraja, Kasinadar
Theoretical investigation on the glycan-binding specificity of Agrocybe cylindracea galectin using molecular modeling and molecular dynamics simulation studies
JOURNAL OF MOLECULAR RECOGNITION, 28:528-538, SEP 2015
abstract, full text, DOI:10.1002/jmr.2468

Lewis, Martin A.; Hunihan, Lisa; Watson, John; Gentles, Robert G.; Hu, Shuanghua; Huang, Yazhong; Bronson, Joanne; Macor, John E.; Beno, Brett R.; Ferrante, Meredith; Hendricson, Adam; Knox, Ronald J.; Molski, Thaddeus F.; Kong, Yan; Cvijic, Mary Ellen; Rockwell, Kristin L.; Weed, Michael R.; Cacace, Angela M.; Westphal, Ryan S.; Alt, Andrew; Brown, Jeffrey M.
Discovery of D1 Dopamine Receptor Positive Allosteric Modulators: Characterization of Pharmacology and Identification of Residues that Regulate Species Selectivity
JOURNAL OF PHARMACOLOGY AND EXPERIMENTAL THERAPEUTICS, 354:340-349, SEP 2015
abstract, full text, DOI:10.1124/jpet.115.224071

Dai, Yuejie; Zhen, Jing; Zhang, Xiuli; Zhong, Yonghui; Liu, Shaodan; Sun, Ziyue; Guo, Yue; Wu, Qingli
Analysis of the complex formation, interaction and electron transfer pathway between the "open" conformation of NADPH-cytochrome P450 reductase and aromatase
STEROIDS, 101:116-124, SEP 2015
abstract, full text, DOI:10.1016/j.steroids.2015.06.006

Marcinkowski, Lukasz; Kloskowski, Adam; Czub, Jacek; Namiesnik, Jacek; Warminska, Dorota
Solvation of ionic liquids based on N-methyl-N-alkyl morpholinium cations in dimethylsulfoxide - volumetric and compressibility studies
JOURNAL OF CHEMICAL THERMODYNAMICS, 88:36-43, SEP 2015
abstract, full text, DOI:10.1016/j.jct.2015.04.006

Alishahi, Marzieh; Kamali, Reza; Abouali, Omid
Rigorous study of molecular dynamics of a single dsDNA confined in a nanochannel: Introduction of a critical mobility behaviour
EUROPEAN PHYSICAL JOURNAL E, 38 Art. No. 92, AUG 31 2015
abstract, full text, DOI:10.1140/epje/i2015-15092-5

Nieto, Carlos T.; Gonzalez-Nunez, Veronica; Rodriguez, Raquel E.; Diez, David; Garrido, Narciso M.
Design, synthesis, pharmacological evaluation and molecular dynamics of beta-amino acids morphan-derivatives as novel ligands for opioid receptors
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 101:150-162, AUG 28 2015
abstract, full text, DOI:10.1016/j.ejmech.2015.06.025

Chen, Xi; Hnida, Kathrin; Graewert, Melissa Ann; Andersen, Jan Terje; Iversen, Rasmus; Tuukkanen, Anne; Svergun, Dmitri; Sollid, Ludvig M.
Structural Basis for Antigen Recognition by Transglutaminase 2-specific Autoantibodies in Celiac Disease
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:21365-21375, AUG 28 2015
abstract, full text, DOI:10.1074/jbc.M115.669895

Xi, Yi-Bo; Chen, Xiang-Jun; Zhao, Wei-Jie; Yan, Yong-Bin
Congenital Cataract-Causing Mutation G129C in gamma C-Crystallin Promotes the Accumulation of Two Distinct Unfolding Intermediates That Form Highly Toxic Aggregates
JOURNAL OF MOLECULAR BIOLOGY, 427:2765-2781, AUG 28 2015
abstract, full text, DOI:10.1016/j.jmb.2015.07.001

Anishkin, Andriy; Vanegas, Juan M.; Rogers, David M.; Lorenzi, Philip L.; Chan, Wai Kin; Purwaha, Preeti; Weinstein, John N.; Sukharev, Sergei; Rempe, Susan B.
Catalytic Role of the Substrate Defines Specificity of Therapeutic L-Asparaginase
JOURNAL OF MOLECULAR BIOLOGY, 427:2867-2885, AUG 28 2015
abstract, full text, DOI:10.1016/j.jmb.2015.06.017

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy
Correlated Conformational Motions of the KH Domains of Far Upstream Element Binding Protein Complexed with Single-Stranded DNA Oligomers
JOURNAL OF PHYSICAL CHEMISTRY B, 119:10998-11009, AUG 27 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b01687

Mondal, Padmabati; Biswas, Mithun; Goldau, Thomas; Heckel, Alexander; Burghardt, Irene
In Search of an Efficient Photoswitch for Functional RNA: Design Principles from a Microscopic Analysis of Azobenzene-linker-RNA Dynamics with Different Linkers
JOURNAL OF PHYSICAL CHEMISTRY B, 119:11275-11286, AUG 27 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03118

Ramirez-Salinas, G. Lizbeth; Michel Espinoza-Fonseca, L.
Atomistic Characterization of the First Step of Calcium Pump Activation Associated with Proton Countertransport
BIOCHEMISTRY, 54:5235-5241, AUG 25 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00672

Heim, Erin N.; Marston, Jez L.; Federman, Ross S.; Edwards, Anne P. B.; Karabadzhak, Alexander G.; Petti, Lisa M.; Engelman, Donald M.; DiMaio, Daniel
Biologically active LIL proteins built with minimal chemical diversity
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E4717-E4725, AUG 25 2015
abstract, full text, DOI:10.1073/pnas.1514230112

Sondergaard, Siri; Aznauryan, Mikayel; Haustrup, Emil K.; Schiott, Birgit; Birkedal, Victoria; Corry, Ben
Dynamics of Fluorescent Dyes Attached to G-Quadruplex DNA and their Effect on FRET Experiments
CHEMPHYSCHEM, 16:2562-2570, AUG 24 2015
abstract, full text, DOI:10.1002/cphc.201500271

Sriwimol, Wilaiwan; Aroonkesorn, Aratee; Sakdee, Somsri; Kanchanawarin, Chalermpol; Uchihashi, Takayuki; Ando, Toshio; Angsuthanasombat, Chanan
Potential Prepore Trimer Formation by the Bacillus thuringiensis Mosquito-specific Toxin MOLECULAR INSIGHTS INTO A CRITICAL PREREQUISITE OF MEMBRANE-BOUND MONOMERS
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:20793-20803, AUG 21 2015
abstract, full text, DOI:10.1074/jbc.M114.627554

Sanchez-Badillo, Joel; Gallo, Marco; Alvarado, Sandra; Glossman-Mitnik, Daniel
Solvation Thermodynamic Properties of Hydrogen Sulfide in [C(4)mim][PF6], [C(4)mim][BF4], and (C(4)mim][Cl] Ionic Liquids, Determined by Molecular Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:10727-10737, AUG 20 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b06525

Shi, Wei; Siefert, Nicholas S.; Morreale, Bryan D.
Molecular Simulations of CO2, H-2, H2O, and H2S Gas Absorption into Hydrophobic Poly(dimethylsiloxane) (PDMS) Solvent: Solubility and Surface Tension
JOURNAL OF PHYSICAL CHEMISTRY C, 119:19253-19265, AUG 20 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b05806

Gorny, Krzysztof; Raczynski, Przemyslaw; Dendzik, Zbigniew; Gburski, Zygmunt
Odd-Even Effects in the Dynamics of Liquid Crystalline Thin Films on the Surface of Single Walled Carbon and Silicon Carbide Nanotubes: Computer Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY C, 119:19266-19271, AUG 20 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b05961

Lee, One-Sun; Carignano, Marcelo A.
Exfoliation of Electrolyte-Intercalated Graphene: Molecular Dynamics Simulation Study
JOURNAL OF PHYSICAL CHEMISTRY C, 119:19415-19422, AUG 20 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b03217

Tan, Bikan; Hodak, Miroslav; Lu, Wenchang; Bernholc, J.
Charge transport in DNA nanowires connected to carbon nanotubes
PHYSICAL REVIEW B, 92 Art. No. 075429, AUG 19 2015
abstract, full text, DOI:10.1103/PhysRevB.92.075429

Luitz, Manuel; Bomblies, Rainer; Ostermeir, Katja; Zacharias, Martin
Exploring biomolecular dynamics and interactions using advanced sampling methods
JOURNAL OF PHYSICS-CONDENSED MATTER, 27 Art. No. 323101, AUG 19 2015
abstract, full text, DOI:10.1088/0953-8984/27/32/323101

Pluhackova, Kristyna; Boeckmann, Rainer A.
Biomembranes in atomistic and coarse-grained simulations
JOURNAL OF PHYSICS-CONDENSED MATTER, 27 Art. No. 323103, AUG 19 2015
abstract, full text, DOI:10.1088/0953-8984/27/32/323103

Jones, Paul R.; Hao, Xiuqing; Cruz-Chu, Eduardo R.; Rykaczewski, Konrad; Nandy, Krishanu; Schutzius, Thomas M.; Varanasi, Kripa K.; Megaridis, Constantine M.; Walther, Jens H.; Koumoutsakos, Petros; Espinosa, Horacio D.; Patankar, Neelesh A.
Sustaining dry surfaces under water
SCIENTIFIC REPORTS, 5 Art. No. 12311, AUG 18 2015
abstract, full text, DOI:10.1038/srep12311

Watly, Joanna; Simonovsky, Eyal; Barbosa, Nuno; Spodzieja, Marta; Wieczorek, Robert; Rodziewicz-Motowidlo, Sylwia; Miller, Yifat; Kozlowski, Henryk
African Viper Poly-His Tag Peptide Fragment Efficiently Binds Metal Ions and Is Folded into an alpha-Helical Structure
INORGANIC CHEMISTRY, 54:7692-7702, AUG 17 2015
abstract, full text, DOI:10.1021/acs.inorgchem.5b01029

Mino-Galaz, German A.; Gutierrez, Gonzalo
Hydrogen bonds and asymmetrical heat diffusion in alpha-helices. A computational analysis
CHEMICAL PHYSICS LETTERS, 635:16-22, AUG 16 2015
abstract, full text, DOI:10.1016/j.cplett.2015.06.041

Raczynski, Przemyslaw; Raczynska, Violetta; Gorny, Krzysztof; Gburski, Zygmunt
Properties of ultrathin cholesterol and phospholipid layers surrounding silicon-carbide nanotube: MD simulations
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 580:22-30, AUG 15 2015
abstract, full text, DOI:10.1016/j.abb.2015.06.008

MacDonald, Corey A.; Boyd, Russell J.
Computational insights into the suicide inhibition of Plasmodium falciparum Fk506-binding protein 35
BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 25:3221-3225, AUG 15 2015
abstract, full text, DOI:10.1016/j.bmcl.2015.05.079

Mahdavi, Somayeh; Kuyucak, Serdar
Mechanism of Ion Permeation in Mammalian Voltage-Gated Sodium Channels
PLOS ONE, 10 Art. No. e0133000, AUG 14 2015
abstract, full text, DOI:10.1371/journal.pone.0133000

Zidar, Nace; Macut, Helena; Tomasic, Tihomir; Brvar, Matjaz; Montalvao, Sofia; Tammela, Paivi; Solmajer, Tom; Masic, Lucija Peterlin; Ilas, Janez; Kikelj, Danijel
N-Phenyl-4,5-dibromopyrrolamides and N-Phenylindolamides as ATP Competitive DNA Gyrase B Inhibitors: Design, Synthesis, and Evaluation
JOURNAL OF MEDICINAL CHEMISTRY, 58:6179-6194, AUG 13 2015
abstract, full text, DOI:10.1021/acs.jmedchem.5b00775

Kurnikov, Igor V.; Kurnikova, Maria
Modeling Electronic Polarizability Changes in the Course of a Magnesium Ion Water Ligand Exchange Process
JOURNAL OF PHYSICAL CHEMISTRY B, 119:10275-10286, AUG 13 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b01295

La Penna, Giovanni; Hureau, Christelle; Faller, Peter
Learning chemistry with multiple first-principles simulations
MOLECULAR SIMULATION, 41:780-787, AUG 13 2015
abstract, full text, DOI:10.1080/08927022.2014.927064

Koishi, Takahiro; Takeichi, Hironori
An efficiently extendable and fine-grain parallelised molecular dynamics simulation program: Mid
MOLECULAR SIMULATION, 41:801-807, AUG 13 2015
abstract, full text, DOI:10.1080/08927022.2014.923569

Nomura, Kentaro; Oikawa, Minoru; Kawai, Atsushi; Narumi, Tetsu; Yasuoka, Kenji
GPU-accelerated replica exchange molecular simulation on solid-liquid phase transition study of Lennard-Jones fluids
MOLECULAR SIMULATION, 41:874-880, AUG 13 2015
abstract, full text, DOI:10.1080/08927022.2014.954572

Kang, Hojin; Klauda, Jeffery B.
Molecular dynamics simulations of palmitoyloleoylphosphatidylglycerol bilayers
MOLECULAR SIMULATION, 41:948-954, AUG 13 2015
abstract, full text, DOI:10.1080/08927022.2014.926548

Mori, Yoshiharu; Okumura, Hisashi
Molecular dynamics simulation study on the high-pressure behaviour of an AK16 peptide
MOLECULAR SIMULATION, 41:1035-1040, AUG 13 2015
abstract, full text, DOI:10.1080/08927022.2014.938071

Sadeghian, Keyarash; Ochsenfeld, Christian
Unraveling the Base Excision Repair Mechanism of Human DNA Glycosylase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:9824-9831, AUG 12 2015
abstract, full text, DOI:10.1021/jacs.5b01449

Kostopoulou, Ourania N.; Magoulas, George E.; Papadopoulos, Georgios E.; Mouzaki, Athanasia; Dinos, George P.; Papaioannou, Dionissios; Kalpaxis, Dimitrios L.
Synthesis and Evaluation of Chloramphenicol Homodimers: Molecular Target, Antimicrobial Activity, and Toxicity against Human Cells
PLOS ONE, 10 Art. No. e0134526, AUG 12 2015
abstract, full text, DOI:10.1371/journal.pone.0134526

Raina, Deepak; Agarwal, Praveen; Lee, James; Bharti, Ajit; McKnight, C. James; Sharma, Pankaj; Kharbanda, Surender; Kufe, Donald
Characterization of the MUC1-C Cytoplasmic Domain as a Cancer Target
PLOS ONE, 10 Art. No. e0135156, AUG 12 2015
abstract, full text, DOI:10.1371/journal.pone.0135156

Nagy-Smith, Katelyn; Moore, Eric; Schneider, Joel; Tycko, Robert
Molecular structure of monomorphic peptide fibrils within a kinetically trapped hydrogel network
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:9816-9821, AUG 11 2015
abstract, full text, DOI:10.1073/pnas.1509313112

Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stephanie; Aspuru-Guzik, Alan; Kleinekathoefer, Ulrich
Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 119:9995-10004, AUG 6 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03654

Atsmon-Raz, Yoav; Miller, Yifat
A Proposed Atomic Structure of the Self-Assembly of the Non-Amyloid-beta Component of Human alpha-Synuclein As Derived by Computational Tools
JOURNAL OF PHYSICAL CHEMISTRY B, 119:10005-10015, AUG 6 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03760

Di Marino, Daniele; Bonome, Emma Letizia; Tramontano, Anna; Chinappi, Mauro
All-Atom Molecular Dynamics Simulation of Protein Translocation through an alpha-Hemolysin Nanopore
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:2963-2968, AUG 6 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b01077

Vasilevskaya, Tatiana; Khrenova, Maria G.; Nemukhin, Alexander V.; Thiel, Walter
Mechanism of proteolysis in matrix metalloproteinase-2 revealed by QM/MM modeling
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:1621-1630, AUG 5 2015
abstract, full text, DOI:10.1002/jcc.23977

Goh, Boon Chong; Perilla, Juan R.; England, Matthew R.; Heyrana, Katrina J.; Craven, Rebecca C.; Schulten, Klaus
Atomic Modeling of an Immature Retroviral Lattice Using Molecular Dynamics and Mutagenesis
STRUCTURE, 23:1414-1425, AUG 4 2015
abstract, full text, TCBG publications, DOI:10.1016/j.str.2015.05.017

Baday, Sefer; Orabi, Esam A.; Wang, Shihao; Lamoureux, Guillaume; Berneche, Simon
Mechanism of NH4+ Recruitment and NH3 Transport in Rh Proteins
STRUCTURE, 23:1550-1557, AUG 4 2015
abstract, full text, DOI:10.1016/j.str.2015.06.010

Jahed, Zeinab; Shams, Hengameh; Mofrad, Mohammad R. K.
A Disulfide Bond Is Required for the Transmission of Forces through SUN-KASH Complexes
BIOPHYSICAL JOURNAL, 109:501-509, AUG 4 2015
abstract, full text, DOI:10.1016/j.bpj.2015.06.057

Liu, Yufeng; Ke, Meng; Gong, Haipeng
Protonation of Glu(135) Facilitates the Outward-to-Inward Structural Transition of Fucose Transporter
BIOPHYSICAL JOURNAL, 109:542-551, AUG 4 2015
abstract, full text, DOI:10.1016/j.bpj.2015.06.037

Leioatts, Nicholas; Romo, Tod D.; DaniaL, Shairy Azmy; Grossfield, Alan
Retinal Conformation Changes Rhodopsin's Dynamic Ensemble
BIOPHYSICAL JOURNAL, 109:608-617, AUG 4 2015
abstract, full text, DOI:10.1016/j.bpj.2015.06.046

Wells, Stephen A.; van der Kamp, Marc W.; McGeagh, John D.; Mulholland, Adrian J.
Structure and Function in Homodimeric Enzymes: Simulations of Cooperative and Independent Functional Motions
PLOS ONE, 10 Art. No. e0133372, AUG 4 2015
abstract, full text, DOI:10.1371/journal.pone.0133372

Diaz-Franulic, Ignacio; Sepulveda, Romina V.; Navarro-Quezada, Nieves; Gonzalez-Nilo, Fernando; Naranjo, David
Pore dimensions and the role of occupancy in unitary conductance of Shaker K channels
JOURNAL OF GENERAL PHYSIOLOGY, 146:133-146, AUG 2015
abstract, full text, DOI:10.1085/jgp.201411353

Geninatti, Thomas; Hood, R. Lyle; Bruno, Giacomo; Jain, Priya; Nicolov, Eugenia; Ziemys, Arturas; Grattoni, Alessandro
Sustained Administration of Hormones Exploiting Nanoconfined Diffusion through Nanochannel Membranes
MATERIALS, 8:5276-5288, AUG 2015
abstract, full text, DOI:10.3390/ma8085241

Theis, Jeanne L.; Zimmermann, Michael T.; Evans, Jared M.; Eckloff, Bruce W.; Wieben, Eric D.; Qureshi, Muhammad Y.; O'Leary, Patrick W.; Olson, Timothy M.
Recessive MYH6 Mutations in Hypoplastic Left Heart With Reduced Ejection Fraction
CIRCULATION-CARDIOVASCULAR GENETICS, 8:564-571, AUG 2015
abstract, full text, DOI:10.1161/CIRCGENETICS.115.001070

Yuchi, Zhiguang; Yuen, Siobhan M. Wong King; Lau, Kelvin; Underhill, Ainsley Q.; Cornea, Razvan L.; Fessenden, James D.; Van Petegem, Filip
Crystal structures of ryanodine receptor SPRY1 and tandem-repeat domains reveal a critical FKBP12 binding determinant
NATURE COMMUNICATIONS, 6 Art. No. 7947, AUG 2015
abstract, full text, DOI:10.1038/ncomms8947

Ierich, Jessica C. M.; Oliveira, Guedmiller S.; Vig, Ana C. A.; Amarante, Adriano M.; Franca, Eduardo F.; Leite, Fabio L.; Mascarenhas, Yvonne P.
A Computational Protein Structure Refinement of the Yeast Acetohydroxyacid Synthase
JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY, 26:1702-1709, AUG 2015
abstract, full text, DOI:10.5935/0103-5053.20150144

Tepavcevic, Sanja; Liu, Yuzi; Zhou, Dehua; Lai, Barry; Maser, Jorg; Zuo, Xiaobing; Chan, Henry; Kral, Petr; Johnson, Christopher S.; Stamenkovic, Vojislav; Markovic, Nenad M.; Rajh, Tijana
Nanostructured Layered Cathode for Rechargeable Mg-Ion Batteries
ACS NANO, 9:8194-8205, AUG 2015
abstract, full text, DOI:10.1021/acsnano.5b02450

Tse, Amanda; Verkhivker, Germady M.
Molecular Dynamics Simulations and Structural Network Analysis of c-Abl and c-Src Kinase Core Proteins: Capturing Allosteric Mechanisms and Communication Pathways from Residue Centrality
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:1645-1662, AUG 2015
abstract, full text, DOI:10.1021/acs.jcim.5b00240

Verma, Saroj; Debnath, Utsab; Agarwal, Pooja; Srivastava, Kumkum; Prabhakar, Yenamandra S.
In Silico Exploration for New Antimalarials: Arylsulfonyloxy Acetimidamides as Prospective Agents
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:1708-1719, AUG 2015
abstract, full text, DOI:10.1021/acs.jcim.5b00392

Kumar, Rajendra; Grubmueller, Helmut
do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations
BIOINFORMATICS, 31:2583-2585, AUG 1 2015
abstract, full text, DOI:10.1093/bioinformatics/btv190

Omar, Sara Ibrahim; Tuszynski, Jack
Ranking the Binding Energies of p53 Mutant Activators and Their ADMET Properties
CHEMICAL BIOLOGY & DRUG DESIGN, 86:163-172, AUG 2015
abstract, full text, DOI:10.1111/cbdd.12480

Paoletta, Silvia; Sabbadin, Davide; von Kuegelgen, Ivar; Hinz, Sonja; Katritch, Vsevolod; Hoffmann, Kristina; Abdelrahman, Aliaa; Strassburger, Jens; Baqi, Younis; Zhao, Qiang; Stevens, Raymond C.; Moro, Stefano; Mueller, Christa E.; Jacobson, Kenneth A.
Modeling ligand recognition at the P2Y(12) receptor in light of X-ray structural information
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 29:737-756, AUG 2015
abstract, full text, DOI:10.1007/s10822-015-9858-z

Xu, Jinxing; Yuan, Haoliang; Ran, Ting; Zhang, Yanmin; Liu, Haichun; Lu, Shuai; Xiong, Xiao; Xu, Anyang; Jiang, Yulei; Lu, Tao; Chen, Yadong
A selectivity study of sodium-dependent glucose cotransporter 2/sodium-dependent glucose cotransporter 1 inhibitors by molecular modeling
JOURNAL OF MOLECULAR RECOGNITION, 28:467-479, AUG 2015
abstract, full text, DOI:10.1002/jmr.2464

Kong, Ren; Chang, Shan; Xia, Weiming; Wong, Stephen T. C.
Molecular dynamics simulation study reveals potential substrate entry path into gamma-secretase/presenilin-1
JOURNAL OF STRUCTURAL BIOLOGY, 191:120-129, AUG 2015
abstract, full text, DOI:10.1016/j.jsb.2015.07.001

Li Zan; Qi XiaoLe; Ren XianGang; Cui Lei; Wang XiaoMei; Zhu Ping
Molecular characteristics and evolutionary analysis of a very virulent infectious bursal disease virus
SCIENCE CHINA-LIFE SCIENCES, 58:731-738, AUG 2015
abstract, full text, DOI:10.1007/s11427-015-4900-x

Pietra, Francesco
On the Quest of Dioxygen by Monomeric Sarcosine Oxidase. A Molecular Dynamics Investigation
CHEMISTRY & BIODIVERSITY, 12:1163-1171, AUG 2015
abstract, full text, DOI:10.1002/cbdv.201400362

Gabrieli, Andrea; Sant, Marco; Demontis, Pierfranco; Suffritti, Giuseppe B.
Partial Charges in Periodic Systems: Improving Electrostatic Potential (ESP) Fitting via Total Dipole Fluctuations and Multiframe Approaches
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3829-3843, AUG 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00503

Domene, Carmen; Jorgensen, Christian; Vanommeslaeghe, Kenno; Schofield, Christopher J.; MacKerell, Alexander, Jr.
Quantifying the Binding Interaction between the Hypoxia-Inducible Transcription Factor and the von Hippel-Lindau Suppressor
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3946-3954, AUG 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00411

Morales-Quintana, Luis; Alejandra Moya-Leon, Maria; Herrera, Raul
Computational study enlightens the structural role of the alcohol acyltransferase DFGWG motif
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 216, AUG 2015
abstract, full text, DOI:10.1007/s00894-015-2762-6

Barraza, Luis F.; Jimenez, Veronica A.; Alderete, Joel B.
Effect of PEGylation on the Structure and Drug Loading Capacity of PAMAM-G4 Dendrimers: A Molecular Modeling Approach on the Complexation of 5-Fluorouracil with Native and PEGylated PAMAM-G4
MACROMOLECULAR CHEMISTRY AND PHYSICS, 216:1689-1701, AUG 2015
abstract, full text, DOI:10.1002/macp.201500179

Cvijetic, Ilija N.; Tanc, Muhammet; Juranic, Ivan O.; Verbic, Tatjana Z.; Supuran, Claudiu T.; Drakulic, Branko J.
5-Aryl-1H-pyrazole-3-carboxylic acids as selective inhibitors of human carbonic anhydrases IX and XII
BIOORGANIC & MEDICINAL CHEMISTRY, 23:4649-4659, AUG 1 2015
abstract, full text, DOI:10.1016/j.bmc.2015.05.052

Halder, Swagata; Surolia, Avadhesha; Mukhopadhyay, Chaitali
Impact of glycosylation on stability, structure and unfolding of soybean agglutinin (SBA): an insight from thermal perturbation molecular dynamics simulations
GLYCOCONJUGATE JOURNAL, 32:371-384, AUG 2015
abstract, full text, DOI:10.1007/s10719-015-9601-y

Rydzewski, Jakub; Strzalka, Wojciech; Nowak, Wieslaw
Nanomechanics of PCNA: A protein-made DNA sliding clamp
CHEMICAL PHYSICS LETTERS, 634:236-242, AUG 1 2015
abstract, full text, DOI:10.1016/j.cplett.2015.06.027

Jain, Amisha; Tripathi, Pranav; Shrotriya, Aniket; Chaudhary, Ritu; Singh, Ajeet
In silico analysis and modeling of putative T cell epitopes for vaccine design of Toscana virus
3 BIOTECH, 5:497-503, AUG 2015
abstract, full text, DOI:10.1007/s13205-014-0247-4

Mansour-Hendili, Lamisse; Blanchard, Anne; Le Pottier, Nelly; Roncelin, Isabelle; Lourdel, Stephane; Treard, Cyrielle; Gonzalez, Wendy; Vergara-Jaque, Ariela; Morin, Gilles; Colin, Estelle; Holder-Espinasse, Muriel; Bacchetta, Justine; Baudouin, Veronique; Benoit, Stephane; Berard, Etienne; Bourdat-Michel, Guylhene; Bouchireb, Karim; Burtey, Stephane; Cailliez, Mathilde; Cardon, Gerard; Cartery, Claire; Champion, Gerard; Chauveau, Dominique; Cochat, Pierre; Dahan, Karin; De la Faille, Renaud; Debray, Francois-Guillaume; Dehoux, Laurenne; Deschenes, Georges; Desport, Estelle; Devuyst, Olivier; Dieguez, Stella; Emma, Francesco; Fischbach, Michel; Fouque, Denis; Fourcade, Jacques; Francois, Helene; Gilbert-Dussardier, Brigitte; Hannedouche, Thierry; Houillier, Pascal; Izzedine, Hassan; Janner, Marco; Karras, Alexandre; Knebelmann, Bertrand; Lavocat, Marie-Pierre; Lemoine, Sandrine; Leroy, Valerie; Loirat, Chantal; Macher, Marie-Alice; Martin-Coignard, Dominique; Morin, Denis; Niaudet, Patrick; Nivet, Hubert; Nobili, Francois; Novo, Robert; Faivre, Laurence; Rigothier, Claire; Roussey-Kesler, Gwenaelle; Salomon, Remi; Schleich, Andreas; Sellier-Leclerc, Anne-Laure; Soulami, Kenza; Tiple, Aurelien; Ulinski, Tim; Vanhille, Philippe; Van Regemorter, Nicole; Jeunemaitre, Xavier; Vargas-Poussou, Rosa
Mutation Update of the CLCN5 Gene Responsible for Dent Disease 1
HUMAN MUTATION, 36:743-752, AUG 2015
abstract, full text, DOI:10.1002/humu.22804

Fiesel, Fabienne C.; Caulfield, Thomas R.; Moussaud-Lamodiere, Elisabeth L.; Ogaki, Kotaro; Dourado, Daniel F. A. R.; Flores, Samuel C.; Ross, Owen A.; Springer, Wolfdieter
Structural and Functional Impact of Parkinson Disease-Associated Mutations in the E3 Ubiquitin Ligase Parkin
HUMAN MUTATION, 36:774-786, AUG 2015
abstract, full text, DOI:10.1002/humu.22808

Slack, Ryan L.; Spiriti, Justin; Ahn, Jinwoo; Parniak, Michael A.; Zuckerman, Daniel M.; Ishima, Rieko
Structural integrity of the ribonuclease H domain in HIV-1 reverse transcriptase
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1526-1538, AUG 2015
abstract, full text, DOI:10.1002/prot.24843

Azamat, Jafar; Ebrahimzadeh, Alireza Rastkar; Sardroodi, Jaber Jahanbin; Gholinezhad, Leila
Molecular Dynamics Simulation of Nanoporous Graphene as Membrane for Ion Separation Under Induced Electric Field
JOURNAL OF COMPUTATIONAL AND THEORETICAL NANOSCIENCE, 12:1512-1518, AUG 2015
abstract, full text, DOI:10.1166/jctn.2015.3922

Sun, Qian; Zhu, Tao; Wang, Chang-yu; Ma, Ding
Binding of human SWI1 ARID domain to DNA without sequence specificity: A molecular dynamics study
JOURNAL OF HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY-MEDICAL SCIENCES, 35:469-476, AUG 2015
abstract, full text, DOI:10.1007/s11596-015-1455-9

Ferrante, Andrea; Templeton, Megan; Hoffman, Megan; Castellini, Margaret J.
The Thermodynamic Mechanism of Peptide-MHC Class II Complex Formation Is a Determinant of Susceptibility to HLA-DM
JOURNAL OF IMMUNOLOGY, 195:1251-1261, AUG 1 2015
abstract, full text, DOI:10.4049/jimmunol.1402367

Fossati, Sara Maria; Candiani, Simona; Noedl, Marie-Therese; Maragliano, Luca; Pennuto, Maria; Domingues, Pedro; Benfenati, Fabio; Pestarino, Mario; Zullo, Letizia
Identification and Expression of Acetylcholinesterase in Octopus vulgaris Arm Development and Regeneration: a Conserved Role for ACHE?
MOLECULAR NEUROBIOLOGY, 52:45-56, AUG 2015
abstract, full text, DOI:10.1007/s12035-014-8842-2

Sencanski, Milan; Dosen-Micovic, Ljiljana; Sukalovic, Vladimir; Kostic-Rajacic, Sladjana
Theoretical insight into sulfur aromatic interactions with extension to D-2 receptor activation mechanism
STRUCTURAL CHEMISTRY, 26:1139-1149, AUG 2015
abstract, full text, DOI:10.1007/s11224-015-0574-z

Wu, Sangwook; Shim, Joong-Youn; Lee, Chang Jun; Pedersen, Lee G.
Do the crystallographic forms of prethrombin-2 revert to a single form in solution?
BIOPHYSICAL CHEMISTRY, 203:28-32, AUG-SEP 2015
abstract, full text, DOI:10.1016/j.bpc.2015.05.005

Sharma, Vivek; Ala-Vannesluoma, Pauliina; Vattulainen, Ilpo; Wikstrom, Marten; Rog, Tomasz
Role of subunit III and its lipids in the molecular mechanism of cytochrome c oxidase
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1847:690-697, AUG 2015
abstract, full text, DOI:10.1016/j.bbabio.2015.04.007

Gao, Weimin; She, Fenghua; Zhang, Juan; Dumee, Ludovic F.; He, Li; Hodgson, Peter D.; Kong, Lingxue
Understanding water and ion transport behaviour and permeability through poly(amide) thin film composite membrane
JOURNAL OF MEMBRANE SCIENCE, 487:32-39, AUG 1 2015
abstract, full text, DOI:10.1016/j.memsci.2015.03.052

Li, Jing; Newhall, Jillian; Ishiyama, Noboru; Gottardi, Cara; Ikura, Mitsuhiko; Leckband, Deborah E.; Tajkhorshid, Emad
Structural Determinants of the Mechanical Stability of alpha-Catenin
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:18890-18903, JUL 31 2015
abstract, full text, DOI:10.1074/jbc.M115.647941

Hamre, Anne Grethe; Jana, Suvamay; Holen, Matilde Mengkrog; Mathiesen, Geir; Vaeljamaee, Priit; Payne, Christina M.; Sorlie, Morten
Thermodynamic Relationships with Processivity in Serratia marcescens Family 18 Chitinases
JOURNAL OF PHYSICAL CHEMISTRY B, 119:9601-9613, JUL 30 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03817

Hsiao, Ya-Wen; Hedstrom, Magnus
Molecular Dynamics Simulations of NaCl Permeation in Bihydrated Montmorillonite Inter layer Nanopores
JOURNAL OF PHYSICAL CHEMISTRY C, 119:17352-17361, JUL 30 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b01169

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy
Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 045106, JUL 28 2015
abstract, full text, DOI:10.1063/1.4927568

Dinpajooh, Mohammadhasan; Matyushov, Dmitry V.
Free energy of ion hydration: Interface susceptibility and scaling with the ion size
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 044511, JUL 28 2015
abstract, full text, DOI:10.1063/1.4927570

Chiodo, Letizia; Malliavin, Therese E.; Maragliano, Luca; Cottone, Grazia; Ciccotti, Giovanni
A Structural Model of the Human alpha 7 Nicotinic Receptor in an Open Conformation
PLOS ONE, 10 Art. No. e0133011, JUL 24 2015
abstract, full text, DOI:10.1371/journal.pone.0133011

Rosler, Kirsten S.; Mercier, Evan; Andrews, Ian C.; Wieden, Hans-Joachim
Histidine 114 Is Critical for ATP Hydrolysis by the Universally Conserved ATPase YchF
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:18650-18661, JUL 24 2015
abstract, full text, DOI:10.1074/jbc.M114.598227

Gosselin-Badaroudine, Pascal; Moreau, Adrien; Delemotte, Lucie; Cens, Thierry; Collet, Claude; Rousset, Matthieu; Charnet, Pierre; Klein, Michael L.; Chahine, Mohamed
Characterization of the honeybee AmNa(V)1 channel and tools to assess the toxicity of insecticides
SCIENTIFIC REPORTS, 5 Art. No. 12475, JUL 23 2015
abstract, full text, DOI:10.1038/srep12475

Rodriguez, Javier; Dolores Elola, M.
Molecular Dynamics Simulations of Ibuprofen Release from pH-Gated Silica Nanochannels
JOURNAL OF PHYSICAL CHEMISTRY B, 119:8868-8878, JUL 23 2015
abstract, full text, DOI:10.1021/jp505585g

Rahaman, Obaidur; Kalimeri, Maria; Melchionna, Simone; Henin, Jerome; Sterpone, Fabio
Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains
JOURNAL OF PHYSICAL CHEMISTRY B, 119:8939-8949, JUL 23 2015
abstract, full text, DOI:10.1021/jp507571u

Martinez, Anna Victoria; Malolepsza, Edyta; Dominguez, Laura; Lu, Qing; Straub, John E.
Role of Charge and Solvation in the Structure and Dynamics of Alanine-Rich Peptide AKA(2) in AOT Reverse Micelles
JOURNAL OF PHYSICAL CHEMISTRY B, 119:9084-9090, JUL 23 2015
abstract, full text, DOI:10.1021/jp508813n

Silveira, Rodrigo L.; Skaf, Munir S.
Molecular Dynamics Simulations of Family 7 Cellobiohydrolase Mutants Aimed at Reducing Product Inhibition
JOURNAL OF PHYSICAL CHEMISTRY B, 119:9295-9303, JUL 23 2015
abstract, full text, DOI:10.1021/jp509911m

Yu, Hao; Yzeiri, Irena; Hou, Binyang; Chen, Chiu-Hao; Bu, Wei; Vanysek, Petr; Chen, Yu-Sheng; Lin, Binhua; Kral, Petr; Schlossman, Mark L.
Electric Field Effect on Phospholipid Monolayers at an Aqueous-Organic Liquid-Liquid Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 119:9319-9334, JUL 23 2015
abstract, full text, DOI:10.1021/jp5098525

Li, Hui; Ngo, Van; Da Siva, Mauricio Chagas; Salahub, Dennis R.; Callahan, Karen; Roux, Benoit; Noskov, Sergei Yu.
Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field
JOURNAL OF PHYSICAL CHEMISTRY B, 119:9401-9416, JUL 23 2015
abstract, full text, DOI:10.1021/jp510560k

Ahmad, Ashfaq; Cai, Yongfei; Chen, Xingqiang; Shuai, Jianwei; Han, Aidong
Conformational Dynamics of Response Regulator RegX3 from Mycobacterium tuberculosis
PLOS ONE, 10 Art. No. e0133389, JUL 22 2015
abstract, full text, DOI:10.1371/journal.pone.0133389

Huang, Jun; Jones, Bryan J.; Kazlauskas, Romas J.
Stabilization of an alpha/beta-Hydrolase by Introducing Pro line Residues: Salicylic Acid Binding Protein 2 from Tobacco
BIOCHEMISTRY, 54:4330-4341, JUL 21 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00333

McCormick, James W.; Vogel, Pia D.; Wise, John G.
Multiple Drug Transport Pathways through Human P-Glycoprotein
BIOCHEMISTRY, 54:4374-4390, JUL 21 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00018

Gonzalez, Walter G.; Arango, Andres S.; Miksovska, Jaroslava
Amphiphilic Residues 29-44 of DREAM N-Termini Mediate Calmodulin:DREAM Complex Formation
BIOCHEMISTRY, 54:4391-4403, JUL 21 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00251

Capponi, Sara; Heyden, Matthias; Bondar, Ana-Nicoleta; Tobias, Douglas J.; White, Stephen H.
Anomalous behavior of water inside the SecY translocon
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:9016-9021, JUL 21 2015
abstract, full text, DOI:10.1073/pnas.1424483112

VanSchouwen, Bryan; Akimoto, Madoka; Sayadi, Maryam; Fogolari, Federico; Melacini, Giuseppe
Role of Dynamics in the Autoinhibition and Activation of the Hyperpolarization-activated Cyclic Nucleotide-modulated (HCN) Ion Channels
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:17642-17654, JUL 17 2015
abstract, full text, DOI:10.1074/jbc.M115.651877

Song, Hyun Deok; Zhu, Fangqiang
Conformational Changes in Two Inter-Helical Loops of Mhp1 Membrane Transporter
PLOS ONE, 10 Art. No. e0133388, JUL 17 2015
abstract, full text, DOI:10.1371/journal.pone.0133388

Chen, Yu; Bauer, Benedikt W.; Rapoport, Tom A.; Gumbart, James C.
Conformational Changes of the Clamp of the Protein Translocation ATPase SecA
JOURNAL OF MOLECULAR BIOLOGY, 427:2348-2359, JUL 17 2015
abstract, full text, DOI:10.1016/j.jmb.2015.05.003

Espinoza-Fonseca, L. Michel; Autry, Joseph M.; Thomas, David D.
Sarcolipin and phospholamban inhibit the calcium pump by populating a similar metal ion-free intermediate state
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, 463:37-41, JUL 17 2015
abstract, full text, DOI:10.1016/j.bbrc.2015.05.012

Bray, David J.; Walsh, Tiffany R.; Noro, Massimo G.; Notman, Rebecca
Complete Structure of an Epithelial Keratin Dimer: Implications for Intermediate Filament Assembly
PLOS ONE, 10 Art. No. e0132706, JUL 16 2015
abstract, full text, DOI:10.1371/journal.pone.0132706

Chen, Chuanying; Esadze, Alexandre; Zandarashvili, Levani; Dan Nguyen; Pettitt, B. Montgomery; Iwahara, Junji
Dynamic Equilibria of Short-Range Electrostatic Interactions at Molecular Interfaces of Protein-DNA Complexes
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:2733-2737, JUL 16 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b01134

de Veer, Simon J.; Swedberg, Joakim E.; Akcan, Muharrem; Rosengren, K. Johan; Brattsand, Maria; Craik, David J.; Harris, Jonathan M.
Engineered protease inhibitors based on sunflower trypsin inhibitor-1 (SFTI-1) provide insights into the role of sequence and conformation in Laskowski mechanism inhibition
BIOCHEMICAL JOURNAL, 469:243-253, JUL 15 2015
abstract, full text, DOI:10.1042/BJ20150412

Fogolari, Federico; Corazza, Alessandra; Fortuna, Sara; Soler, Miguel Angel; VanSchouwen, Bryan; Brancolini, Giorgia; Corni, Stefano; Melacini, Giuseppe; Esposito, Gennaro
Distance-Based Configurational Entropy of Proteins from Molecular Dynamics Simulations
PLOS ONE, 10 Art. No. e0132356, JUL 15 2015
abstract, full text, DOI:10.1371/journal.pone.0132356

Lemkul, Justin A.; Roux, Benoit; van der Spoel, David; MacKerell, Alexander D., Jr.
Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:1473-1479, JUL 15 2015
abstract, full text, DOI:10.1002/jcc.23937

Bermudez, Marcel; Wolber, Gerhard
Structure versus function-The impact of computational methods on the discovery of specific GPCR-ligands
BIOORGANIC & MEDICINAL CHEMISTRY, 23:3907-3912, JUL 15 2015
abstract, full text, DOI:10.1016/j.bmc.2015.03.026

Trujillo, Kevin; Paoletta, Silvia; Kiselev, Evgeny; Jacobson, Kenneth A.
Molecular modeling of the human P2Y(14) receptor: A template for structure-based design of selective agonist ligands
BIOORGANIC & MEDICINAL CHEMISTRY, 23:4056-4064, JUL 15 2015
abstract, full text, DOI:10.1016/j.bmc.2015.03.042

Deganutti, Giuseppe; Cuzzolin, Alberto; Ciancetta, Antonella; Moro, Stefano
Understanding allosteric interactions in G protein-coupled receptors using Supervised Molecular Dynamics: A prototype study analysing the human A(3) adenosine receptor positive allosteric modulator LUF6000
BIOORGANIC & MEDICINAL CHEMISTRY, 23:4065-4071, JUL 15 2015
abstract, full text, DOI:10.1016/j.bmc.2015.03.039

Chen, Chen; Liu, Yonglan; Zhang, Jin; Zhang, Mingzhen; Zheng, Jie; Teng, Yong; Liang, Guizhao
A quantitative sequence-aggregation relationship predictor applied as identification of self-assembled hexapeptides
CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 145:7-16, JUL 15 2015
abstract, full text, DOI:10.1016/j.chemolab.2015.04.009

Nguyen, Lam T.; Gumbart, James C.; Beeby, Morgan; Jensen, Grant J.
Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E3689-E3698, JUL 14 2015
abstract, full text, DOI:10.1073/pnas.1504281112

Chen, Junmei; Hinckley, Jesse D.; Haberichter, Sandra; Jacobi, Paula; Montgomery, Robert; Flood, Veronica H.; Wong, Randall; Interlandi, Gianluca; Chung, Dominic W.; Lopez, Jose A.; Di Paola, Jorge
Variable content of von Willebrand factor mutant monomer drives the phenotypic variability in a family with von Willebrand disease
BLOOD, 126:262-269, JUL 9 2015
abstract, full text, DOI:10.1182/blood-2014-11-613935

Garcia-Gimenez, Elena; Alcaraz, Antonio; Aguilella-Arzo, Marcel; Aguilella, Vicente M.
Selectivity of Protein Ion Channels and the Role of Buried Charges. Analytical Solutions, Numerical Calculations, and MD Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:8475-8479, JUL 9 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03547

Katti, Dinesh R.; Sharma, Anurag; Pradhan, Shashindra Man; Katti, Kalpana S.
Carbon nanotube proximity influences rice DNA
CHEMICAL PHYSICS, 455:17-22, JUL 9 2015
abstract, full text, DOI:10.1016/j.chemphys.2015.03.015

Li, Rui; Fan, Jianfen; Li, Hui; Yan, Xiliang; Yu, Yi
Dynamic behaviors and transport properties of ethanol molecules in transmembrane cyclic peptide nanotubes
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 015101, JUL 7 2015
abstract, full text, DOI:10.1063/1.4923010

Weber, Adrian C. J.; Burnell, E. Elliott; Meerts, W. Leo; de Lange, Cornelis A.; Dong, Ronald Y.; Muccioli, Luca; Pizzirusso, Antonio; Zannoni, Claudio
Communication: Molecular dynamics and H-1 NMR of n-hexane in liquid crystals
JOURNAL OF CHEMICAL PHYSICS, 143 Art. No. 011103, JUL 7 2015
abstract, full text, DOI:10.1063/1.4923253

van den Biggelaar, Maartje; Madsen, Jesper J.; Faber, Johan H.; Zuurveld, Marleen G.; van der Zwaan, Carmen; Olsen, Ole H.; Stennicke, Henning R.; Mertens, Koen; Meijer, Alexander B.
Factor VIII Interacts with the Endocytic Receptor Low-density Lipoprotein Receptor-related Protein 1 via an Extended Surface Comprising "Hot-Spot" Lysine Residues
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:16463-16476, JUL 3 2015
abstract, full text, DOI:10.1074/jbc.M115.650911

Vasco, Aldrin V.; Perez, Carlos S.; Morales, Fidel E.; Garay, Hilda E.; Vasilev, Dimitar; Gavin, Jose A.; Wessjohann, Ludger A.; Rivera, Daniel G.
Macrocyclization of Peptide Side Chains by the Ugi Reaction: Achieving Peptide Folding and Exocyclic N-Functionalization in One Shot
JOURNAL OF ORGANIC CHEMISTRY, 80:6697-6707, JUL 3 2015
abstract, full text, DOI:10.1021/acs.joc.5b00858

Kaware, Ravindra; Desai, Salil
Molecular dynamics modeling of water nanodroplet spreading on topographically patterned silicon dioxide and silicon nitride substrates
IIE TRANSACTIONS, 47:767-782, JUL 3 2015
abstract, full text, DOI:10.1080/0740817X.2014.973983

Alsamarah, Abdelaziz; LaCuran, Alecander E.; Oelschlaeger, Peter; Hao, Jijun; Luo, Yun
Uncovering Molecular Bases Underlying Bone Morphogenetic Protein Receptor Inhibitor Selectivity
PLOS ONE, 10 Art. No. e0132221, JUL 2 2015
abstract, full text, DOI:10.1371/journal.pone.0132221

Zhang, Yuqi; Young, Ryan M.; Thazhathveetil, Arun K.; Singh, Arunoday P. N.; Liu, Chaoren; Berlin, Yuri A.; Grozema, Ferdinand C.; Lewis, Frederick D.; Ratner, Mark A.; Renaud, Nicolas; Siriwong, Khatcharin; Voityuk, Alexander A.; Wasielewski, Michael R.; Beratan, David N.
Conformationally Gated Charge Transfer in DNA Three-Way Junctions
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:2434-2438, JUL 2 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b00863

Mottin, Melina; Souza, Paulo C. T.; Skaf, Munir S.
Molecular Recognition of PPAR gamma by Kinase Cdk5/p25: Insights from a Combination of Protein-Protein Docking and Adaptive Biasing Force Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:8330-8339, JUL 2 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b04269

Duboue-Dijon, Elise; Laage, Damien
Characterization of the Local Structure in Liquid Water by Various Order Parameters
JOURNAL OF PHYSICAL CHEMISTRY B, 119:8406-8418, JUL 2 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b02936

Ambrosia, Matthew Stanley; Jang, Joonkyung; Ha, Man Yeong
Static and dynamic hydrophobicity on a nano-sized groove/ridge surface
COMPUTERS & FLUIDS, 114:75-83, JUL 2 2015
abstract, full text, DOI:10.1016/j.compfluid.2015.02.010

Chwastyk, Mateusz; Bernaola, Adolfo Poma; Cieplak, Marek
Statistical radii associated with amino acids to determine the contact map: fixing the structure of a type I cohesin domain in the Clostridium thermocellum cellulosome
PHYSICAL BIOLOGY, 12 Art. No. 046002, JUL 2015
abstract, full text, DOI:10.1088/1478-3975/12/4/046002

Petukh, Marharyta; Li, Minghui; Alexov, Emil
Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004276, JUL 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004276

Ramirez-Sarmiento, Cesar A.; Noel, Jeffrey K.; Valenzuela, Sandro L.; Artsimovitch, Irina
Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004379, JUL 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004379

Li, Rongzhong; Macnamara, Lindsay M.; Leuchter, Jessica D.; Alexander, Rebecca W.; Cho, Samuel S.
MD Simulations of tRNA and Aminoacyl-tRNA Synthetases: Dynamics, Folding, Binding, and Allostery
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 16:15872-15902, JUL 2015
abstract, full text, DOI:10.3390/ijms160715872

Goryashchenko, Alexander S.; Khrenova, Maria G.; Bochkova, Anna A.; Ivashina, Tatiana V.; Vinokurov, Leonid M.; Savitsky, Alexander P.
Genetically Encoded FRET-Sensor Based on Terbium Chelate and Red Fluorescent Protein for Detection of Caspase-3 Activity
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 16:16642-16654, JUL 2015
abstract, full text, DOI:10.3390/ijms160716642

Schwerdt, Julian G.; MacKenzie, Katrin; Wright, Frank; Oehme, Daniel; Wagner, John M.; Harvey, Andrew J.; Shirley, Neil J.; Burton, Rachel A.; Schreiber, Miriam; Halpin, Claire; Zimmer, Jochen; Marshall, David F.; Waugh, Robbie; Fincher, Geoffrey B.
Evolutionary Dynamics of the Cellulose Synthase Gene Superfamily in Grasses
PLANT PHYSIOLOGY, 168:968-983, JUL 2015
abstract, full text, DOI:10.1104/pp.15.00140

Zeng Yan; Zhang Yong; Song XianQiang; Ji QingHua; Ye Sheng; Zhang RongGuang; Lou JiZhong
The conformational states of talin autoinhibition complex and its activation under forces
SCIENCE CHINA-LIFE SCIENCES, 58:694-703, JUL 2015
abstract, full text, DOI:10.1007/s11427-015-4873-9

Malmstrom, Robert D.; Kornev, Alexandr P.; Taylor, Susan S.; Amaro, Rommie E.
Allostery through the computational microscope: cAMP activation of a canonical signalling domain
NATURE COMMUNICATIONS, 6 Art. No. 7588, JUL 2015
abstract, full text, DOI:10.1038/ncomms8588

Castillo, Juan P.; Rui, Huan; Basilio, Daniel; Das, Avisek; Roux, Benoit; Latorre, Ramon; Bezanilla, Francisco; Holmgren, Miguel
Mechanism of potassium ion uptake by the Na+/K+-ATPase
NATURE COMMUNICATIONS, 6 Art. No. 7622, JUL 2015
abstract, full text, DOI:10.1038/ncomms8622

Clemens, Jonathon B.; Kibar, Osman; Chachisvilis, Mirianas
A molecular propeller effect for chiral separation and analysis
NATURE COMMUNICATIONS, 6 Art. No. 7868, JUL 2015
abstract, full text, DOI:10.1038/ncomms8868

Tamura, Koichi; Hayashi, Shigehiko
Linear Response Path Following: A Molecular Dynamics Method To Simulate Global Conformational Changes of Protein upon Ligand Binding
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2900-2917, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00120

Chen, Nanhao; Zhao, Yuan; Lu, Jianing; Wu, Ruibo; Cao, Zexing
Mechanistic Insights into the Rate-Limiting Step in Purine-Specific Nucleoside Hydrolase
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3180-3188, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00045

Wan, Shunzhou; Knapp, Bernhard; Wright, David W.; Deane, Charlotte M.; Coveney, Peter V.
Rapid, Precise, and Reproducible Prediction of Peptide-MHC Binding Affinities from Molecular Dynamics That Correlate Well with Experiment
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3346-3356, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00179

Moral, M.; Son, W. -J.; Sancho-Garcia, J. C.; Oivier, Y.; Muccioli, L.
Cost-Effective Force Field Tailored for Solid-Phase Simulations of OLED Materials
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3383-3392, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00164

Di Marino, Daniele; Chillemi, Giovanni; De Rubeis, Silvia; Tramontano, Anna; Achsel, Tilmann; Bagni, Claudia
MD and Docking Studies Reveal That the Functional Switch of CYFIP1 is Mediated by a Butterfly-like Motion
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3401-3410, JUL 2015
abstract, full text, DOI:10.1021/ct500431h

Cortes-Ciriano, Isidro; Bouvier, Guillaume; Nilges, Michael; Maragliano, Luca; Malliavin, Therese E.
Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3446-3454, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00153

Walczewska-Szewc, Katarzyna; Depazes, Evelyne; Corry, Ben
Comparing the Ability of Enhanced Sampling Molecular Dynamics Methods To Reproduce the Behavior of Fluorescent Labels on Proteins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3455-3465, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00205

Park, Soohyung; Beayen, Andrew H.; Klauda, Jeffery B.; Im, Wonpil
How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets?
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3466-3477, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00232

Kimanius, Dari; Pettersson, Ingrid; Schluckebier, Gerd; Lindahl, Erik; Andersson, Magnus
SAXS-Guided Metadynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3491-3498, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00299

Robertson, Michael J.; Tirado-Rives, Julian; Jorgensen, William L.
Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:3499-3509, JUL 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00356

Xu, Xuefei; Zheng, Jingjing; Truhlar, Donald G.
Ultraviolet Absorption Spectrum of Malonaldehyde in Water Is Dominated by Solvent-Stabilized Conformations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:8026-8029, JUL 1 2015
abstract, full text, DOI:10.1021/jacs.5b04845

Ficici, Emel; Andricioaei, Ioan; Howorka, Stefan
Dendrimers in Nanoscale Confinement: The Interplay between Conformational Change and Nanopore Entrance
NANO LETTERS, 15:4822-4828, JUL 2015
abstract, full text, DOI:10.1021/acs.nanolett.5b01960

Arias, Hugo R.; Feuerbach, Dominik; Ortells, Marcelo
Functional and structural interaction of (-)-lobeline with human alpha 4 beta 2 and alpha 4 beta 4 nicotinic acetylcholine receptor subtypes
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 64:15-24, JUL 2015
abstract, full text, DOI:10.1016/j.biocel.2015.03.003

Mucic, Ivana D.; Nikolic, Milan R.; Stojanovic, Srdan D.
Contribution of cation-pi interactions to the stability of Sm/LSm oligomeric assemblies
PROTOPLASMA, 252:947-958, JUL 2015
abstract, full text, DOI:10.1007/s00709-014-0727-8

Gao, Yi; Olsen, Kenneth W.
Drug-Polymer Interactions at Water-Crystal Interfaces and Implications for Crystallization Inhibition: Molecular Dynamics Simulations of Amphiphilic Block Copolymer Interactions with Tolazamide Crystals
JOURNAL OF PHARMACEUTICAL SCIENCES, 104:2132-2141, JUL 2015
abstract, full text, DOI:10.1002/jps.24442

Mascayano, Carolina; Espinosa, Victoria; Sepulveda-Boza, Silvia; Hoobler, Eric K.; Perry, Steve; Diaz, Giovanni; Holman, Theodore R.
Enzymatic Studies of Isoflavonoids as Selective and Potent Inhibitors of Human Leukocyte 5-Lipo-Oxygenase
CHEMICAL BIOLOGY & DRUG DESIGN, 86:894-901, JUL 2015
abstract, full text, DOI:10.1111/cbdd.12469

Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji
GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 5:310-323, JUL-AUG 2015
abstract, full text, DOI:10.1002/wcms.1220

Mangiatordi, Giuseppe Felice; Alberga, Domenico; Siragusa, Lydia; Goracci, Laura; Lattanzi, Gianluca; Nicolotti, Orazio
Challenging AQP4 druggability for NMO-IgG antibody binding using molecular dynamics and molecular interaction fields
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:1462-1471, JUL 2015
abstract, full text, DOI:10.1016/j.bbamem.2015.03.019

Garate, Jose Antonio; Stoecki, Johannes; del Carmen Fernandez-Alonso, Maria; Artner, Daniel; Haegman, Mira; Oostenbrink, Chris; Jimenez-Barbero, Jesus; Beyaert, Rudi; Heine, Holger; Kosma, Paul; Zamyatina, Alla
Anti-endotoxic activity and structural basis for human MD-2 center dot TLR4 antagonism of tetraacylated lipid A mimetics based on beta GlcN(1 <-> 1)alpha GlcN scaffold
INNATE IMMUNITY, 21:490-503, JUL 2015
abstract, full text, DOI:10.1177/1753425914550426

Weng, Lindong; Elliott, Gloria D.
Distinctly Different Glass Transition Behaviors of Trehalose Mixed with Na2HPO4 or NaH2PO4: Evidence for its Molecular Origin
PHARMACEUTICAL RESEARCH, 32:2217-2228, JUL 2015
abstract, full text, DOI:10.1007/s11095-014-1610-1

Sharpe, Laura J.; Rao, Geetha; Jones, Peter M.; Glancey, Elizabeth; Aleidi, Shereen M.; George, Anthony M.; Brown, Andrew J.; Gelissen, Ingrid C.
Cholesterol sensing by the ABCG1 lipid transporter: Requirement of a CRAC motif in the final transmembrane domain
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS, 1851:956-964, JUL 2015
abstract, full text, DOI:10.1016/j.bbalip.2015.02.016

Glaser, Jens; Trung Dac Nguyen; Anderson, Joshua A.; Lui, Pak; Spiga, Filippo; Millan, Jaime A.; Morse, David C.; Glotzer, Sharon C.
Strong scaling of general-purpose molecular dynamics simulations on GPUs
COMPUTER PHYSICS COMMUNICATIONS, 192:97-107, JUL 2015
abstract, full text, DOI:10.1016/j.cpc.2015.02.028

Brown, Aaron H.; Walsh, Tiffany R.
An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture
COMPUTER PHYSICS COMMUNICATIONS, 192:278-281, JUL 2015
abstract, full text, DOI:10.1016/j.cpc.2015.02.025

Guerra, Fernando P.; Reyes, Luz; Vergara-Jaque, Ariela; Campos-Hernandez, Carola; Gutierrez, Adelina; Perez-Diaz, Jorge; Perez-Diaz, Ricardo; Blaudez, Damien; Ruiz-Lara, Simon
Populus deltoides Kunitz trypsin inhibitor 3 confers metal tolerance and binds copper, revealing a new defensive role against heavy metal stress
ENVIRONMENTAL AND EXPERIMENTAL BOTANY, 115:28-37, JUL 2015
abstract, full text, DOI:10.1016/j.envexpbot.2015.02.005

Hu, Benfeng; Ge, Zhenpeng; Li, Xiaoyi
Interface Adsorption Taking the Most Advantageous Conformation for Electron Transfer Between Graphene and Cytochrome c
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY, 15:4863-4869, JUL 2015
abstract, full text, DOI:10.1166/jnn.2015.9853

Prigozhin, Maxim B.; Chao, Shu-Han; Sukenik, Shahar; Pogorelov, Taras V.; Gruebele, Martin
Mapping fast protein folding with multiple-site fluorescent probes
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:7966-7971, JUN 30 2015
abstract, full text, DOI:10.1073/pnas.1422683112

Drake, Justin A.; Pettitt, B. Montgomery
Force field-dependent solution properties of glycine oligomers
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:1275-1285, JUN 30 2015
abstract, full text, DOI:10.1002/jcc.23934

Cluxton, Christopher D.; Caffrey, Brian E.; Kinsella, Gemma K.; Moynagh, Paul N.; Fares, Mario A.; Fallon, Padraic G.
Functional conservation of an ancestral Pellino protein in helminth species
SCIENTIFIC REPORTS, 5 Art. No. 11687, JUN 29 2015
abstract, full text, DOI:10.1038/srep11687

Takemoto, Mizuki; Kato, Hideaki E.; Koyama, Michio; Ito, Jumpei; Kamiya, Motoshi; Hayashi, Shigehiko; Maturana, Andres D.; Deisseroth, Karl; Ishitani, Ryuichiro; Nureki, Osamu
Molecular Dynamics of Channelrhodopsin at the Early Stages of Channel Opening
PLOS ONE, 10 Art. No. e0131094, JUN 26 2015
abstract, full text, DOI:10.1371/journal.pone.0131094

Caceres-Delpiano, Javier; Teneb, Jaime; Mansilla, Rodrigo; Garcia, Apolinaria; Salas-Burgos, Alexis
Variations in periplasmic loop interactions determine the pH-dependent activity of the hexameric urea transporter UreI from Helicobacter pylori: a molecular dynamics study
BMC STRUCTURAL BIOLOGY, 15 Art. No. 11, JUN 26 2015
abstract, full text, DOI:10.1186/s12900-015-0038-0

Fuerst, Oliver; Lin, Yibin; Granell, Meritxell; Leblanc, Gerard; Padros, Esteve; Lorenz-Fonfria, Victor A.; Cladera, Josep
The Melibiose Transporter of Escherichia coli CRITICAL CONTRIBUTION OF LYS-377 TO THE STRUCTURAL ORGANIZATION OF THE INTERACTING SUBSTRATE BINDING SITES
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:16261-16271, JUN 26 2015
abstract, full text, DOI:10.1074/jbc.M115.642678

Baylon, Javier L.; Tajkhorshid, Emad
Capturing Spontaneous Membrane Insertion of the Influenza Virus Hemagglutinin Fusion Peptide
JOURNAL OF PHYSICAL CHEMISTRY B, 119:7882-7893, JUN 25 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b02135

Cao, Ruyin; Wu, Shanshan
In silico properties characterization of water-soluble gamma-cyclodextrin bi-capped C-60 complex: Free energy and geometrical insights for stability and solubility
CARBOHYDRATE POLYMERS, 124:188-195, JUN 25 2015
abstract, full text, DOI:10.1016/j.carbpol.2015.02.014

Nishihara, Yasutaka; Kitao, Akio
Gate-controlled proton diffusion and protonation-induced ratchet motion in the stator of the bacterial flagellar motor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:7737-7742, JUN 23 2015
abstract, full text, DOI:10.1073/pnas.1502991112

Boczek, Edgar E.; Reefschlaeger, Lasse G.; Dehling, Marco; Struller, Tobias J.; Haeusler, Elisabeth; Seidl, Andreas; Kaila, Ville R. I.; Buchner, Johannes
Conformational processing of oncogenic v-Src kinase by the molecular chaperone Hsp90
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E3189-E3198, JUN 23 2015
abstract, full text, DOI:10.1073/pnas.1424342112

Luan, Binquan; Huynh, Tien; Zhou, Ruhong
Simplified TiO2 force fields for studies of its interaction with biomolecules
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 234102, JUN 21 2015
abstract, full text, DOI:10.1063/1.4922618

Gu, Ying; Zhou, Hong; Gan, Yichao; Zhang, Jiawei; Chen, Jianghua; Gan, Xiaoxian; Li, Hongzhi; Zheng, Weiwei; Meng, Zhipeng; Ma, Xiaoxiao; Wang, Xichun; Xu, Xiaohua; Xu, Ganyu; Lu, Xiaoya; Liang, Yun; Zhang, Xuzhao; Lu, Xinliang; Huang, Wendong; Xu, Rongzhen
Small-molecule induction of phospho-eIF4E sumoylation and degradation via targeting its phosphorylated serine 209 residue
ONCOTARGET, 6:15111-15121, JUN 20 2015
abstract, full text

Gao, Feng; Kight, Alicia D.; Henderson, Rory; Jayanthi, Srinivas; Patel, Parth; Murchison, Marissa; Sharma, Priyanka; Goforth, Robyn L.; Kumar, Thallapuranam Krishnaswamy Suresh; Henry, Ralph L.; Heyes, Colin D.
Regulation of Structural Dynamics within a Signal Recognition Particle Promotes Binding of Protein Targeting Substrates
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:15462-15474, JUN 19 2015
abstract, full text, DOI:10.1074/jbc.M114.624346

Amin, Muhamed; Vogt, Leslie; Szejgis, Witold; Vassiliev, Serguei; Brudvig, Gary W.; Bruce, Doug; Gunner, M. R.
Proton-Coupled Electron Transfer During the S-State Transitions of the Oxygen-Evolving Complex of Photosystem II
JOURNAL OF PHYSICAL CHEMISTRY B, 119:7366-7377, JUN 18 2015
abstract, full text, DOI:10.1021/jp510948e

Plehn, Thomas; Ziemann, Dirk; Megow, Joerg; May, Volkhard
Frenkel to Wannier-Mott Exciton Transition: Calculation of FRET Rates for a Tubular Dye Aggregate Coupled to a CdSe Nanocrystal
JOURNAL OF PHYSICAL CHEMISTRY B, 119:7467-7472, JUN 18 2015
abstract, full text, DOI:10.1021/jp5111696

Kokhan, Oleksandr; Ponomarenko, Nina S.; Pokkuluri, P. Raj; Schiffer, Marianne; Mulfort, Karen L.; Tiede, David. M.
Bidirectional Photoinduced Electron Transfer in Ruthenium(II)-Tris-bipyridyl-Modified PpcA, a Multi-heme c-Type Cytochrome from Geobacter sulfurreducens
JOURNAL OF PHYSICAL CHEMISTRY B, 119:7612-7624, JUN 18 2015
abstract, full text, DOI:10.1021/jp511558f

Holland, Bryan W.; Berry, Mark D.; Gray, C. G.; Tomberli, Bruno
A Permeability Study of O-2 and the Trace Amine p-Tyramine through Model Phosphatidylcholine Bilayers
PLOS ONE, 10 Art. No. e0122468, JUN 18 2015
abstract, full text, DOI:10.1371/journal.pone.0122468

Guvench, Olgun
Revealing the mechanisms of protein disorder and N-glycosylation in CD44-hyaluronan binding using molecular simulation
FRONTIERS IN IMMUNOLOGY, 6:1-9, JUN 16 2015
abstract, full text, DOI:10.3389/fimmu.2015.00305

Tse, Amanda; Verkhivker, Gennady M.
Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution
PLOS ONE, 10 Art. No. e0130203, JUN 15 2015
abstract, full text, DOI:10.1371/journal.pone.0130203

Shen Zhuang-Lin; He Gao-Hong; Zhang Ning; Hao Ce
Molecular Dynamics Simulation of Reverse-Osmotic Salt Rejection and Water Transport through Double-Walled Carbon Nanotube
ACTA PHYSICO-CHIMICA SINICA, 31:1025-1034, JUN 15 2015
abstract, full text, DOI:10.3866/PKU.WHXB201504141

Tian, He; Sakmar, Thomas P.; Huber, Thomas
Micelle-Enhanced Bioorthogonal Labeling of Genetically Encoded Azido Groups on the Lipid-Embedded Surface of a GPCR
CHEMBIOCHEM, 16:1314-1322, JUN 15 2015
abstract, full text, DOI:10.1002/cbic.201500030

Weng, Lindong; Chen, Cong; Li, Weizhong
Calorimetric and molecular simulation study on unfrozen water characteristics in aqueous sugar solutions: implications for biopreservation
MOLECULAR SIMULATION, 41:691-698, JUN 13 2015
abstract, full text, DOI:10.1080/08927022.2014.917299

Li, Junwei; Lu, Shouqin; Liu, Yuzhi; Pang, Chunli; Chen, Yafei; Zhang, Suhua; Yu, Hui; Long, Mian; Zhang, Hailin; Logothetis, Diomedes E.; Zhan, Yong; An, Hailong
Identification of the Conformational transition pathway in PIP2 Opening Kir Channels
SCIENTIFIC REPORTS, 5 Art. No. 11289, JUN 11 2015
abstract, full text, DOI:10.1038/srep11289

Espinoza-Fonseca, L. Michel; Ramirez-Salinas, G. Lizbeth
Microsecond Molecular Simulations Reveal a Transient Proton Pathway in the Calcium Pump
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:7055-7058, JUN 10 2015
abstract, full text, DOI:10.1021/jacs.5b03814

Wirth, Anna Jean; Liu, Yaxin; Prigozhin, Maxim B.; Schulten, Klaus; Gruebele, Martin
Comparing Fast Pressure Jump and Temperature Jump Protein Folding Experiments and Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:7152-7159, JUN 10 2015
abstract, full text, TCBG publications, DOI:10.1021/jacs.5b02474

Yao, Kai; Tan, Pengli; Luo, Yinchan; Feng, Liangzhu; Xu, Ligeng; Liu, Zhuang; Li, Youyong; Peng, Rui
Graphene Oxide Selectively Enhances Thermostability of Trypsin
ACS APPLIED MATERIALS & INTERFACES, 7:12270-12277, JUN 10 2015
abstract, full text, DOI:10.1021/acsami.5b03118

Cheng, Mary Hongying; Block, Ethan; Hu, Feizhuo; Cobanoglu, Murat Can; Sorkin, Alexander; Bahar, Ivet
Insights into the modulation of dopamine transporter function by amphetamine, orphenadrine, and cocaine binding
FRONTIERS IN NEUROLOGY, 6 Art. No. UNSP 134, JUN 9 2015
abstract, full text, DOI:10.3389/fneur.2015.00134

Bakalis, Evangelos; Hoefinger, Siegfried; Venturini, Alessandro; Zerbetto, Francesco
Crossover of two power laws in the anomalous diffusion of a two lipid membrane
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 215102, JUN 7 2015
abstract, full text, DOI:10.1063/1.4921891

Wang, Conan K.; Northfield, Susan E.; Swedberg, Joakim E.; Colless, Barbara; Chaousis, Stephanie; Price, David A.; Liras, Spiros; Craik, David J.
Exploring experimental and computational markers of cyclic peptides: Charting islands of permeability
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 97:202-213, JUN 5 2015
abstract, full text, DOI:10.1016/j.ejmech.2015.04.049

Cao Ping; Luo Cheng-Lin; Chen Gui-Hu; Han Dian-Rong; Zhu Xing-Feng; Dai Ya-Fei
Flux controllable pumping of water molecules in a double-walled carbon nanotube
ACTA PHYSICA SINICA, 64 Art. No. 116101, JUN 5 2015
abstract, full text, DOI:10.7498/aps.64.116101

Mei, Ye; Simmonett, Andrew C.; Pickard, Frank C.; DiStasio, Robert A., Jr.; Brooks, Bernard R.; Shao, Yihan
Numerical Study on the Partitioning of the Molecular Polarizability into Fluctuating Charge and Induced Atomic Dipole Contributions
JOURNAL OF PHYSICAL CHEMISTRY A, 119:5865-5882, JUN 4 2015
abstract, full text, DOI:10.1021/acs.jpca.5b03159

Gorczyca, Marcelina; Korchowiec, Beata; Korchowiec, Jacek; Trojan, Sonia; Rubio-Magnieto, Jenifer; Luis, Santiago V.; Rogalska, Ewa
A Study of the Interaction between a Family of Gemini Amphiphilic Pseudopeptides and Model Monomolecular Film Membranes Formed with a Cardiolipin
JOURNAL OF PHYSICAL CHEMISTRY B, 119:6668-6679, JUN 4 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b02575

Schonbeck, Christian; Li, Hui; Han, Bao-Hang; Laursen, Bo W.
Solvent Effects and Driving Forces in Pillararene Inclusion Complexes
JOURNAL OF PHYSICAL CHEMISTRY B, 119:6711-6720, JUN 4 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b02515

Muecksch, Christian; Roesch, Christina; Mueller-Renno, Christine; Ziegler, Christiane; Urbassek, Herbert M.
Consequences of Hydrocarbon Contamination for Wettability and Protein Adsorption on Graphite Surfaces
JOURNAL OF PHYSICAL CHEMISTRY C, 119:12496-12501, JUN 4 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b02948

Balme, Sebastien; Picaud, Fabien; Manghi, Manoel; Palmeri, John; Bechelany, Mikhael; Cabello-Aguilar, Simon; Abou-Chaaya, Adib; Miele, Philippe; Balanzat, Emmanuel; Janot, Jean Marc
Ionic transport through sub-10 nm diameter hydrophobic high-aspect ratio nanopores: experiment, theory and simulation
SCIENTIFIC REPORTS, 5 Art. No. 10135, JUN 3 2015
abstract, full text, DOI:10.1038/srep10135

Farhi, Emmanuel; Ferran, Ghislain; Haeck, Wim; Pellegrini, Eric; Calzavara, Yoann
Light and heavy water dynamic structure factor for neutron transport codes
JOURNAL OF NUCLEAR SCIENCE AND TECHNOLOGY, 52:844-856, JUN 3 2015
abstract, full text, DOI:10.1080/00223131.2014.984002

Suzuki, Takashi; Suzuki, Miho; Ogino, Shinji; Umemoto, Ryo; Nishida, Noritaka; Shimada, Ichio
Mechanical force effect on the two-state equilibrium of the hyaluronan-binding domain of CD44 in cell rolling
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:6991-6996, JUN 2 2015
abstract, full text, DOI:10.1073/pnas.1423520112

Ieong, Pek; Amaro, Rommie E.; Li, Wilfred W.
Molecular Dynamics Analysis of Antibody Recognition and Escape by Human H1N1 Influenza Hemagglutinin
BIOPHYSICAL JOURNAL, 108:2704-2712, JUN 2 2015
abstract, full text, DOI:10.1016/j.bpj.2015.04.025

Kinde, Monica N.; Chen, Qiang; Lawless, Matthew J.; Mowrey, David D.; Xu, Jiawei; Saxena, Sunil; Xu, Yan; Tang, Pei
Conformational Changes Underlying Desensitization of the Pentameric Ligand-Gated Ion Channel ELIC
STRUCTURE, 23:995-1004, JUN 2 2015
abstract, full text, DOI:10.1016/j.str.2015.03.017

Park, Hahnbeom; DiMaio, Frank; Baker, David
The Origin of Consistent Protein Structure Refinement from Structural Averaging
STRUCTURE, 23:1123-1128, JUN 2 2015
abstract, full text, DOI:10.1016/j.str.2015.03.022

Gong Lin-Chen; Zhou Xin; Ouyang Zhong-Can
Reweighted ensemble dynamics simulations: Theory, improvement, and application
CHINESE PHYSICS B, 24 Art. No. 060202, JUN 2015
abstract, full text, DOI:10.1088/1674-1056/24/6/060202

Priya, Prerna; Maity, Atanu; Majumdar, Sarmistha; Dastidar, Shubhra Ghosh
Interactions between Bcl-xl and its inhibitors: Insights into ligand design from molecular dynamics simulations
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 59:1-13, JUN 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.02.005

Supunyabut, Chirayut; Fuklang, Sunit; Sompornpisut, Pornthep
Continuum electrostatic approach for evaluating positions and interactions of proteins in a bilayer membrane
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 59:81-91, JUN 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.04.003

Merino, Felipe; Bouvier, Benjamin; Cojocaru, Vlad
Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. UNSP e1004287, JUN 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004287

Kai, Tianhan; Zhang, Lin; Wang, Xiaoying; Jing, Aihua; Zhao, Bingqing; Yu, Xiang; Zheng, Jie; Zhou, Feimeng
Tabersonine Inhibits Amyloid Fibril Formation and Cytotoxicity of A beta(1-42)
ACS CHEMICAL NEUROSCIENCE, 6:879-888, JUN 2015
abstract, full text, DOI:10.1021/acschemneuro.5b00015

Woll, Kellie A.; Weiser, Brian P.; Liang, Qiansheng; Meng, Tao; McKinstry-Wu, Andrew; Pinch, Benika; Dailey, William P.; Gao, Wei Dong; Covarrubias, Manuel; Eckenhoff, Roderic G.
Role for the Propofol Hydroxyl in Anesthetic Protein Target Molecular Recognition
ACS CHEMICAL NEUROSCIENCE, 6:927-935, JUN 2015
abstract, full text, DOI:10.1021/acschemneuro.5b00078

Mortier, Jeremie; Rakers, Christin; Bermudez, Marcel; Murgueitio, Manuela S.; Riniker, Sereina; Wolber, Gerhard
The impact of molecular dynamics on drug design: applications for the characterization of ligand-macromolecule complexes
DRUG DISCOVERY TODAY, 20:686-702, JUN 2015
abstract, full text, DOI:10.1016/j.drudis.2015.01.003

Guerra, Federico; Bondar, Ana-Nicoleta
Dynamics of the Plasma Membrane Proton Pump
JOURNAL OF MEMBRANE BIOLOGY, 248:443-453, JUN 2015
abstract, full text, DOI:10.1007/s00232-014-9732-2

Vermaas, Josh V.; Baylon, Javier L.; Arcario, Mark J.; Muller, Melanie P.; Wu, Zhe; Pogorelov, Taras V.; Tajkhorshid, Emad
Efficient Exploration of Membrane-Associated Phenomena at Atomic Resolution
JOURNAL OF MEMBRANE BIOLOGY, 248:563-582, JUN 2015
abstract, full text, DOI:10.1007/s00232-015-9806-9

Vanatta, Dan K.; Shukla, Diwakar; Lawrenz, Morgan; Pande, Vijay S.
A network of molecular switches controls the activation of the two-component response regulator NtrC
NATURE COMMUNICATIONS, 6 Art. No. 7283, JUN 2015
abstract, full text, DOI:10.1038/ncomms8283

Pontiggia, F.; Pachov, D. V.; Clarkson, M. W.; Villali, J.; Hagan, M. F.; Pande, V. S.; Kern, D.
Free energy landscape of activation in a signalling protein at atomic resolution
NATURE COMMUNICATIONS, 6 Art. No. 7284, JUN 2015
abstract, full text, DOI:10.1038/ncomms8284

Chintapalli, Sree V.; Bhardwaj, Gaurav; Patel, Reema; Shah, Natasha; Patterson, Randen L.; van Rossum, Damian B.; Anishkin, Andriy; Adams, Sean H.
Molecular Dynamic Simulations Reveal the Structural Determinants of Fatty Acid Binding to Oxy-Myoglobin
PLOS ONE, 10 Art. No. e0128496, JUN 1 2015
abstract, full text, DOI:10.1371/journal.pone.0128496

Elder, Robert M.; Pfaendtner, Jim; Jayaraman, Arthi
Effect of Hydrophobic and Hydrophilic Surfaces on the Stability of Double-Stranded DNA
BIOMACROMOLECULES, 16:1862-1869, JUN 2015
abstract, full text, DOI:10.1021/acs.biomac.5b00469

Ioannidis, Dimitris; Papadopoulos, Georgios E.; Anastassopoulos, Georgios; Kortsaris, Alexandros; Anagnostopoulos, Konstantinos
Structural properties and interaction energies affecting drug design. An approach combining molecular simulations, statistics, interaction energies and neural networks
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 56:7-12, JUN 2015
abstract, full text, DOI:10.1016/j.compbiolchem.2015.02.016

Ramming, Thomas; Okumura, Masaki; Kanemura, Shingo; Baday, Sefer; Birk, Julia; Moes, Suzette; Spiess, Martin; Jenoe, Paul; Berneche, Simon; Inaba, Kenji; Appenzeller-Herzog, Christian
A PDI-catalyzed thiol-disulfide switch regulates the production of hydrogen peroxide by human Ero1
FREE RADICAL BIOLOGY AND MEDICINE, 83:361-372, JUN 2015
abstract, full text, DOI:10.1016/j.freeradbiomed.2015.02.011

Smith, David J.; Shah, Jindal K.; Maginn, Edward J.
Molecular Dynamics Simulation Study of the Association of Lidocainium Docusate and Its Derivatives in Aqueous Solution
MOLECULAR PHARMACEUTICS, 12:1893-1901, JUN 2015
abstract, full text, DOI:10.1021/mp5005993

Lagardere, Louis; Lipparini, Filippo; Polack, Etienne; Stamm, Benjamin; Cances, Eric; Schnieders, Michael; Ren, Pengyu; Maday, Yvon; Piquemal, Jean-Philip
Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II. Toward Massively Parallel Computations Using Smooth Particle Mesh Ewald
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2589-2599, JUN 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00171

Pronk, Sander; Pouya, Iman; Lundborg, Magnus; Rotskoff, Grant; Wesen, Bjorn; Kasson, Peter M.; Lindahl, Erik
Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2600-2608, JUN 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00234

Jefferys, Elizabeth; Sands, Zara A.; Shi, Jiye; Sansom, Mark S. P.; Fowler, Philip W.
Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2743-2754, JUN 2015
abstract, full text, DOI:10.1021/ct501111d

Costa, Mauricio G. S.; Batista, Paulo R.; Bisch, Paulo M.; Perahia, David
Exploring Free Energy Landscapes of Large Conformational Changes: Molecular Dynamics with Excited Normal Modes
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2755-2767, JUN 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00003

Meyer, Tim; Knapp, Ernst-Walter
pK(a) Values in Proteins Determined by Electrostatics Applied to Molecular Dynamics Trajectories
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2827-2840, JUN 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00123

Devi, Meena J.
Molecular simulations of mixed self-assembled monolayer coated gold nanoparticles in water
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 149, JUN 2015
abstract, full text, DOI:10.1007/s00894-015-2684-3

Guan, Li-Jun; Ohtsuka, Jun; Okai, Masahiko; Miyakawa, Takuya; Mase, Tomoko; Zhi, Yuehua; Hou, Feng; Ito, Noriyuki; Iwasaki, Akira; Yasohara, Yoshihiko; Tanokura, Masaru
A new target region for changing the substrate specificity of amine transaminases
SCIENTIFIC REPORTS, 5 Art. No. 10753, JUN 1 2015
abstract, full text, DOI:10.1038/srep10753

Zhan, Yingqian Ada; Ytreberg, F. Marty
The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 575:22-29, JUN 1 2015
abstract, full text, DOI:10.1016/j.abb.2015.03.021

Li, Yang; Gong, Haipeng
Theoretical and simulation studies on voltage-gated sodium channels
PROTEIN & CELL, 6:413-422, JUN 2015
abstract, full text, DOI:10.1007/s13238-015-0152-6

Caliman, Alisha D.; Swift, Sara E.; Wang, Yi; Miao, Yinglong; McCammon, J. Andrew
Investigation of the conformational dynamics of the apo A(2A) adenosine receptor
PROTEIN SCIENCE, 24:1004-1012, JUN 2015
abstract, full text, DOI:10.1002/pro.2681

Mironov, Vladimir A.; Khrenova, Maria G.; Lychko, Leonora A.; Nemukhin, Alexander V.
Computational characterization of the chemical step in the GTP hydrolysis by Ras-GAP for the wild-type and G13V mutated Ras
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1046-1053, JUN 2015
abstract, full text, DOI:10.1002/prot.24802

Kapoor, Abhijeet; Travesset, Alex
Differential dynamics of RAS isoforms in GDP- and GTP-bound states
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1091-1106, JUN 2015
abstract, full text, DOI:10.1002/prot.24805

Abdizadeh, Haleh; Atilgan, Ali Rana; Atilgan, Canan
Detailed molecular dynamics simulations of human transferrin provide insights into iron release dynamics at serum and endosomal pH
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 20:705-718, JUN 2015
abstract, full text, DOI:10.1007/s00775-015-1256-4

Morales-Camilo, Nicole; Salas, Cristian O.; Sanhueza, Claudia; Espinosa-Bustos, Christian; Sepulveda-Boza, Silvia; Reyes-Parada, Miguel; Gonzalez-Nilo, Fernando; Caroli-Rezende, Marcos; Fierro, Angelica
Synthesis, Biological Evaluation, and Molecular Simulation of Chalcones and Aurones as Selective MAO-B Inhibitors
CHEMICAL BIOLOGY & DRUG DESIGN, 85:685-695, JUN 2015
abstract, full text, DOI:10.1111/cbdd.12458

Zima, Vlastimil; Witschas, Katja; Hynkova, Anna; Zimova, Lucie; Barvik, Ivan; Vlachova, Viktorie
Structural modeling and patch-clamp analysis of pain-related mutation TRPA1-N855S reveal inter-subunit salt bridges stabilizing the channel open state
NEUROPHARMACOLOGY, 93:294-307, JUN 2015
abstract, full text, DOI:10.1016/j.neuropharm.2015.02.018

Bishop, Kevin P.; Constable, Steve; Faruk, Nabil F.; Roy, Pierre-Nicholas
OpenMM accelerated MMTK
COMPUTER PHYSICS COMMUNICATIONS, 191:203-208, JUN 2015
abstract, full text, DOI:10.1016/j.cpc.2015.01.025

Stolzenberg, Sebastian; Quick, Matthias; Zhao, Chunfeng; Gotfryd, Kamil; Khelashvili, George; Gether, Ulrik; Loland, Claus J.; Javitch, Jonathan A.; Noskov, Sergei; Weinstein, Harel; Shi, Lei
Mechanism of the Association between Na+ Binding and Conformations at the Intracellular Gate in Neurotransmitter: Sodium Symporters
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:13992-14003, MAY 29 2015
abstract, full text, DOI:10.1074/jbc.M114.625343

Abriata, Luciano A.; Dal Peraro, Matteo
Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding
SCIENTIFIC REPORTS, 5 Art. No. 10549, MAY 29 2015
abstract, full text, DOI:10.1038/srep10549

Karacheytsev, Maksym V.; Gladchenko, Galina O.; Andrushchenko, Valery; Leontiev, Victor S.; Karachevtsev, Victor A.
Hybridization of Homopolynucleotides with Different Base Ordering on the Carbon Nanotube Surface
JOURNAL OF PHYSICAL CHEMISTRY C, 119:11991-12001, MAY 28 2015
abstract, full text, DOI:10.1021/acs.jpcc.5b02114

Blank, Iris D.; Sadeghian, Keyarash; Ochsenfeld, Christian
A Base-Independent Repair Mechanism for DNA Glycosylase-No Discrimination Within the Active Site
SCIENTIFIC REPORTS, 5 Art. No. 10369, MAY 27 2015
abstract, full text, DOI:10.1038/srep10369

Mendoza-Martinez, Cesar; Correa-Basurto, Jose; Nieto-Meneses, Rocio; Marquez-Navarro, Adrian; Aguilar-Suarez, Rocio; Dinora Montero-Cortes, Miriam; Nogueda-Torres, Benjamin; Suarez-Contreras, Erick; Galindo-Sevilla, Norma; Rojas-Rojas, Angela; Rodriguez-Lezama, Alejandro; Hernandez-Luis, Francisco
Design, synthesis and biological evaluation of quinazoline derivatives as anti-trypanosomatid and anti-plasmodial agents
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 96:296-307, MAY 26 2015
abstract, full text, DOI:10.1016/j.ejmech.2015.04.028

Bacolla, Albino; Zhu, Xiao; Chen, Hanning; Howells, Katy; Cooper, David N.; Vasquez, Karen M.
Local DNA dynamics shape mutational patterns of mononucleotide repeats in human genomes
NUCLEIC ACIDS RESEARCH, 43:5065-5080, MAY 26 2015
abstract, full text, DOI:10.1093/nar/gkv364

Karain, Wael I.; Qaraeen, Nael I.
Weighted protein residue networks based on joint recurrences between residues
BMC BIOINFORMATICS, 16 Art. No. 173, MAY 26 2015
abstract, full text, DOI:10.1186/s12859-015-0621-1

Merget, Benjamin; Sotriffer, Christoph A.
Slow-Onset Inhibition of Mycobacterium tuberculosis InhA: Revealing Molecular Determinants of Residence Time by MD Simulations
PLOS ONE, 10 Art. No. e0127009, MAY 21 2015
abstract, full text, DOI:10.1371/journal.pone.0127009

Yu, Yi; Fan, Jianfen; Yan, Mang; Xu, Jian; Zhang, Mingming
Tilt Behavior of an Octa-Peptide Nanotube in POPE and Affects on the Transport Characteristics of Channel Water
JOURNAL OF PHYSICAL CHEMISTRY A, 119:4723-4734, MAY 21 2015
abstract, full text, DOI:10.1021/acs.jpca.5b01380

Faller, Christina E.; Guvench, Olgun
Sulfation and Cation Effects on the Conformational Properties of the Glycan Backbone of Chondroitin Sulfate Disaccharides
JOURNAL OF PHYSICAL CHEMISTRY B, 119:6063-6073, MAY 21 2015
abstract, full text, DOI:10.1021/jp511431q

Hadi-Alijanvand, Hamid; Rouhani, Maryam
Journey of Poly-Nucleotides through OmpF Porin
JOURNAL OF PHYSICAL CHEMISTRY B, 119:6113-6128, MAY 21 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00763

Vermaas, Josh V.; Crowley, Michael F.; Beckham, Gregg T.; Payne, Christina M.
Effects of Lytic Polysaccharide Monooxygenase Oxidation on Cellulose Structure and Binding of Oxidized Cellulose Oligomers to Cellulases
JOURNAL OF PHYSICAL CHEMISTRY B, 119:6129-6143, MAY 21 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00778

Mino-Galaz, German A.
Allosteric Communication Pathways and Thermal Rectification in PDZ-2 Protein: A Computational Study
JOURNAL OF PHYSICAL CHEMISTRY B, 119:6179-6189, MAY 21 2015
abstract, full text, DOI:10.1021/acs.jpcb.5602228

Padhi, Siladitya; Priyakumar, U. Deva
Ion Hydration Dynamics in Conjunction with a Hydrophobic Gating Mechanism Regulates Ion Permeation in p7 Viroporin from Hepatitis C Virus
JOURNAL OF PHYSICAL CHEMISTRY B, 119:6204-6210, MAY 21 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b02759

Izgu, Enver Cagri; Fahrenbach, Albert C.; Zhang, Na; Li, Li; Zhang, Wen; Larsen, Aaron T.; Blain, J. Craig; Szostak, Jack W.
Uncovering the Thermodynamics of Monomer Binding for RNA Replication
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:6373-6382, MAY 20 2015
abstract, full text, DOI:10.1021/jacs.5b02707

Ureta-Zanartu, M. Soledad; Mascayano, Carolina; Gutierrez, Claudio
On the dramatic increase with chain length of the oxidazability of linear saturated aliphatic alcohols on gold in alkaline media
ELECTROCHIMICA ACTA, 165:232-238, MAY 20 2015
abstract, full text, DOI:10.1016/j.electacta.2015.02.230

Patra, Swarna M.; Chakraborty, Sudip; Shahane, Ganesh; Prasanna, Xavier; Sengupta, Durba; Maiti, Prabal K.; Chattopadhyay, Amitabha
Differential dynamics of the serotonin(1A) receptor in membrane bilayers of varying cholesterol content revealed by all atom molecular dynamics simulation
MOLECULAR MEMBRANE BIOLOGY, 32:127-137, MAY 19 2015
abstract, full text, DOI:10.3109/09687688.2015.1096971

Modarres, Hassan Pezeshgi; Dorokhov, Boris D.; Popov, Vladimir O.; Ravin, Nikolai V.; Skryabin, Konstantin G.; Dal Peraro, Matteo
Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519
BIOCHEMISTRY, 54:3076-3085, MAY 19 2015
abstract, full text, DOI:10.1021/bi501227b

Biocca, Silvia; Iacovelli, Federico; Matarazzo, Sara; Vindigni, Giulia; Oteri, Francesco; Desideri, Alessandro; Falconi, Mattia
Molecular mechanism of statin-mediated LOX-1 inhibition
CELL CYCLE, 14:1583-1595, MAY 19 2015
abstract, full text, DOI:10.1080/15384101.2015.1026486

Khadka, Nawal K.; Cheng, Xiaolin; Ho, Chian Sing; Katsaras, John; Pan, Jianjun
Interactions of the Anticancer Drug Tamoxifen with Lipid Membranes
BIOPHYSICAL JOURNAL, 108:2492-2501, MAY 19 2015
abstract, full text, DOI:10.1016/j.bpj.2015.04.010

Bykhovskaia, Maria
Calcium Binding Promotes Conformational Flexibility of the Neuronal Ca2+ Sensor Synaptotagmin
BIOPHYSICAL JOURNAL, 108:2507-2520, MAY 19 2015
abstract, full text, DOI:10.1016/j.bpj.2015.04.007

Pavsic, Miha; Ilc, Gregor; Vidmar, Tilen; Plavec, Janez; Lenarcic, Brigita
The cytosolic tail of the tumor marker protein Trop2-a structural switch triggered by phosphorylation
SCIENTIFIC REPORTS, 5 Art. No. 10324, MAY 18 2015
abstract, full text, DOI:10.1038/srep10324

Stachiewicz, Anna; Molski, Andrzej
A Coarse-Grained MARTINI-Like Force Field for DNA Unzipping in Nanopores
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:947-956, MAY 15 2015
abstract, full text, DOI:10.1002/jcc.23874

Krieger, Elmar; Vriend, Gert
New Ways to Boost Molecular Dynamics Simulations
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:996-1007, MAY 15 2015
abstract, full text, DOI:10.1002/jcc.23899

Bureau, Hailey R.; Merz, Dale R., Jr.; Hershkovits, Eli; Quirk, Stephen; Hernandez, Rigoberto
Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents
PLOS ONE, 10 Art. No. e0127034, MAY 13 2015
abstract, full text, DOI:10.1371/journal.pone.0127034

Lu, Songsong; Xin, Ying; Tang, Xiaolong; Yue, Feng; Wang, Huihui; Bai, Yucheng; Niu, Yonggang; Chen, Qiang
Differences in Hematological Traits between High- and Low-Altitude Lizards (Genus Phrynocephalus)
PLOS ONE, 10 Art. No. e0125751, MAY 8 2015
abstract, full text, DOI:10.1371/journal.pone.0125751

Zhang, Yu-Hang; Shetty, Keerthi; Surleac, Marius D.; Petrescu, Andrei J.; Schatz, David G.
Mapping and Quantitation of the Interaction between the Recombination Activating Gene Proteins RAG1 and RAG2
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:11802-11817, MAY 8 2015
abstract, full text, DOI:10.1074/jbc.M115.638627

Impellizzeri, Agata Antonina Rita; Pappalardo, Matteo; Basile, Livia; Manfra, Ornella; Andressen, Kjetil Wessel; Krobert, Kurt Allen; Messina, Angela; Levy, Finn Olav; Guccione, Salvatore
Identification of essential residues for binding and activation in the human 5-HT7(a) serotonin receptor by molecular modeling and site-directed mutagenesis
FRONTIERS IN BEHAVIORAL NEUROSCIENCE, 9 Art. No. 92, MAY 8 2015
abstract, full text, DOI:10.3389/fnbeh.2015.00092

Bonome, Emma Letizia; Lepore, Rosalba; Raimondo, Domenico; Cecconi, Fabio; Tramontano, Anna; Chinappi, Mauro
Multistep Current Signal in Protein Translocation through Graphene Nanopores
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5815-5823, MAY 7 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b02172

Jahiruddin, Sk; Datta, Ayan
What Sustains the Unnatural Base Pairs (UBPs) with No Hydrogen Bonds
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5839-5845, MAY 7 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b03293

Landry, Markita P.; Vukovic, Lela; Kruss, Sebastian; Bisker, Gili; Landry, Alexandra M.; Islam, Shahrin; Jain, Rishabh; Schulten, Klaus; Strano, Michael S.
Comparative Dynamics and Sequence Dependence of DNA and RNA Binding to Single Walled Carbon Nanotubes
JOURNAL OF PHYSICAL CHEMISTRY C, 119:10048-10058, MAY 7 2015
abstract, full text, TCBG publications, DOI:10.1021/jp511448e

Ruiz, Luis; Benjamin, Ari; Sullivan, Matthew; Keten, Sinan
Regulating Ion Transport in Peptide Nanotubes by Tailoring the Nanotube Lumen Chemistry
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:1514-1520, MAY 7 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b00252

Sieradzan, Adam K.
Introduction of Periodic Boundary Conditions into UNRES Force Field
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:940-946, MAY 5 2015
abstract, full text, DOI:10.1002/jcc.23864

Cui, Fengchao; Yang, Kecheng; Li, Yunqi
Investigate the Binding of Catechins to Trypsin Using Docking and Molecular Dynamics Simulation
PLOS ONE, 10 Art. No. e0125848, MAY 4 2015
abstract, full text, DOI:10.1371/journal.pone.0125848

Azamat, Jafar; Khataee, Alireza; Joob, Sang Woo
Molecular dynamics simulation of trihalomethanes separation from water by functionalized nanoporous graphene under induced pressure
CHEMICAL ENGINEERING SCIENCE, 127:285-292, MAY 4 2015
abstract, full text, DOI:10.1016/j.ces.2015.01.048

Ko, Jeong-Ahn; Ambrosia, Matthew; Ha, Man Yeong
A study of the wetting characteristics of a nano-sized water droplet on heterogeneous striped surfaces
COMPUTERS & FLUIDS, 112:19-34, MAY 2 2015
abstract, full text, DOI:10.1016/j.compfluid.2015.02.005

Oehme, Daniel P.; Downton, Matthew T.; Doblin, Monika S.; Wagner, John; Gidley, Michael J.; Bacic, Antony
Unique Aspects of the Structure and Dynamics of Elementary I beta Cellulose Microfibrils Revealed by Computational Simulations
PLANT PHYSIOLOGY, 168:3-U654, MAY 2015
abstract, full text, DOI:10.1104/pp.114.254664

Wall, Jonathan S.; Martin, Emily B.; Richey, Tina; Stuckey, Alan C.; Macy, Sallie; Wooliver, Craig; Williams, Angela; Foster, James S.; McWilliams-Koeppen, Penney; Uberbacher, Ed; Cheng, Xiaolin; Kennel, Stephen J.
Preclinical Validation of the Heparin-Reactive Peptide p5+14 as a Molecular Imaging Agent for Visceral Amyloidosis
MOLECULES, 20:7657-7682, MAY 2015
abstract, full text, DOI:10.3390/molecules20057657

Sinko, Robert; Keten, Sinan
Traction-separation laws and stick-slip shear phenomenon of interfaces between cellulose nanocrystals
JOURNAL OF THE MECHANICS AND PHYSICS OF SOLIDS, 78:526-539, MAY 2015
abstract, full text, DOI:10.1016/j.jmps.2015.02.012

Fukuda, Masahiro; Takeda, Hironori; Kato, Hideaki E.; Doki, Shintaro; Ito, Koichi; Maturana, Andres D.; Ishitani, Ryuichiro; Nureki, Osamu
Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK
NATURE COMMUNICATIONS, 6 Art. No. 7097, MAY 2015
abstract, full text, DOI:10.1038/ncomms8097

Kato, Hideaki E.; Kamiya, Motoshi; Sugo, Seiya; Ito, Jumpei; Taniguchi, Reiya; Orito, Ayaka; Hirata, Kunio; Inutsuka, Ayumu; Yamanaka, Akihiro; Maturana, Andres D.; Ishitani, Ryuichiro; Sudo, Yuki; Hayashi, Shigehiko; Nureki, Osamu
Atomistic design of microbial opsin-based blue-shifted optogenetics tools
NATURE COMMUNICATIONS, 6 Art. No. 7177, MAY 2015
abstract, full text, DOI:10.1038/ncomms8177

Calvaresi, Matteo; Furini, Simone; Domene, Carmen; Bottoni, Andrea; Zerbetto, Francesco
Blocking the Passage: C-60 Geometrically Clogs K+ Channels
ACS NANO, 9:4827-4834, MAY 2015
abstract, full text, DOI:10.1021/nn506164s

Yan, Xiliang; Fan, Jianfen; Yu, Yi; Xu, Jian; Zhang, Mingming
Transport Behavior of a Single Ca2+, K+, and Na+ in a Water-Filled Transmembrane Cyclic Peptide Nanotube
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:998-1011, MAY 2015
abstract, full text, DOI:10.1021/acs.jcim.5b00025

Rashid, M. Harunur; Heinzelmann, Germano; Kuyucak, Serdar
Calculation of free energy changes due to mutations from alchemical free energy simulations
JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY, 14 Art. No. 1550023, MAY 2015
abstract, full text, DOI:10.1142/S0219633615500236

Zheng, Wenjun; Qin, Feng
A combined coarse-grained and all-atom simulation of TRPV1 channel gating and heat activation
JOURNAL OF GENERAL PHYSIOLOGY, 145:443-456, MAY 2015
abstract, full text, DOI:10.1085/jgp.201411335

Akcapinar, Gunseli Bayram; Venturini, Alessandro; Martelli, Pier Luigi; Casadio, Rita; Sezerman, Ugur O.
Modulating the thermostability of Endoglucanase I from Trichoderma reesei using computational approaches
PROTEIN ENGINEERING DESIGN & SELECTION, 28:127-135, MAY 2015
abstract, full text, DOI:10.1093/protein/gzv012

Wassenaar, Tsjerk A.; Ingolfsson, Helgi I.; Boeckmann, Rainer A.; Tieleman, D. Peter; Marrink, Siewert J.
Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2144-2155, MAY 2015
abstract, full text, DOI:10.1021/acs.jctc.5b00209

Jo, Sunhwan; Chipot, Christophe; Roux, Benoit
Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:2234-2244, MAY 2015
abstract, full text, DOI:10.1021/ct501034w

Feng, Zhiwei; Ma, Shifan; Hu, Guanxing; Xie, Xiang-Qun
Allosteric Binding Site and Activation Mechanism of Class C G-Protein Coupled Receptors: Metabotropic Glutamate Receptor Family
AAPS JOURNAL, 17:737-753, MAY 2015
abstract, full text, DOI:10.1208/s12248-015-9742-8

Feig, Michael; Harada, Ryuhei; Mori, Takaharu; Yu, Isseki; Takahashi, Koichi; Sugita, Yuji
Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 58:1-9, MAY 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.02.004

Hill, Benjamin L.; Wong, Jennifer; May, Brian M.; Huerta, Fidel B.; Manley, Tara E.; Sullivan, Peter R. F.; Olsen, Kenneth W.; Ballicora, Miguel A.
Conserved residues of the Pro103-Arg115 loop are involved in triggering the allosteric response of the Escherichia coli ADP-glucose pyrophosphorylase
PROTEIN SCIENCE, 24:714-728, MAY 2015
abstract, full text, DOI:10.1002/pro.2644

Khoa Pham; Dhulipala, Gangadhar; Gonzalez, Walter G.; Gerstman, Bernard S.; Regmi, Chola; Chapagain, Prem P.; Miksovska, Jaroslava
Ca2+ and Mg2+ modulate conformational dynamics and stability of downstream regulatory element antagonist modulator
PROTEIN SCIENCE, 24:741-751, MAY 2015
abstract, full text, DOI:10.1002/pro.2646

Harrison, Reed E. S.; Gorham, Ronald D., Jr.; Morikis, Dimitrios
Energetic evaluation of binding modes in the C3d and Factor H (CCP 19-20) complex
PROTEIN SCIENCE, 24:789-802, MAY 2015
abstract, full text, DOI:10.1002/pro.2650

Samadani, Ramin; Zhang, Jun; Brophy, Amanda; Oashi, Taiji; Priyakumar, U. Deva; Raman, E. Prabhu; St John, Franz J.; Jung, Kwan-Young; Fletcher, Steven; Pozharski, Edwin; MacKerell, Alexander D., Jr.; Shapiro, Paul
Small-molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf
BIOCHEMICAL JOURNAL, 467:425-438, MAY 1 2015
abstract, full text, DOI:10.1042/BJ20131571

Nanda, Hirsh; Heinrich, Frank; Loesche, Mathias
Membrane association of the PTEN tumor suppressor: Neutron scattering and MD simulations reveal the structure of protein-membrane complexes
METHODS, 77-78:136-146, MAY 1 2015
abstract, full text, DOI:10.1016/j.ymeth.2014.10.014

Prakash, Priyanka; Hancock, John F.; Gorfe, Alemayehu A.
Binding hotspots on K-ras: Consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:898-909, MAY 2015
abstract, full text, DOI:10.1002/prot.24786

Sharp, Kim A.; O'Brien, Evan; Kasinath, Vignesh; Wand, A. Joshua
On the relationship between NMR-derived amide order parameters and protein backbone entropy changes
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:922-930, MAY 2015
abstract, full text, DOI:10.1002/prot.24789

Khelashvili, George; Doktorova, Milka; Sahai, Michelle A.; Johner, Niklaus; Shi, Lei; Weinstein, Harel
Computational modeling of the N-terminus of the human dopamine transporter and its interaction with PIP2-containing membranes
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:952-969, MAY 2015
abstract, full text, DOI:10.1002/prot.24792

Tsai, Hui-Hsu Gavin; Lee, Jian-Bin; Li, Hung-Sheng; Hou, Tsai-Yi; Chu, Wen-Yuan; Shen, Po-Chuan; Chen, Ying-Yu; Tan, Chun-Jui; Hu, Jia-Cheng; Chiu, Chih-Chiang
Geometrical effects of phospholipid olefinic bonds on the structure and dynamics of membranes: A molecular dynamics study
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:1234-1247, MAY 2015
abstract, full text, DOI:10.1016/j.bbamem.2015.02.016

Akcapinar, Gunseli Bayram; Kappel, Lisa; Sezerman, Osman Ugur; Seidl-Seiboth, Verena
Molecular diversity of LysM carbohydrate-binding motifs in fungi
CURRENT GENETICS, 61:103-113, MAY 2015
abstract, full text, DOI:10.1007/s00294-014-0471-9

Jackson, Brian C.; Reigan, Philip; Miller, Bettina; Thompson, David C.; Vasiliou, Vasilis
Human ALDH1B1 Polymorphisms may Affect the Metabolism of Acetaldehyde and All-trans retinaldehyde-In Vitro Studies and Computational Modeling
PHARMACEUTICAL RESEARCH, 32:1648-1662, MAY 2015
abstract, full text, DOI:10.1007/s11095-014-1564-3

Gaete-Eastman, Carlos; Morales-Quintana, Luis; Herrera, Raul; Alejandra Moya-Leon, Maria
In-silico analysis of the structure and binding site features of an alpha-expansin protein from mountain papaya fruit (VpEXPA2), through molecular modeling, docking, and dynamics simulation studies
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 115, MAY 2015
abstract, full text, DOI:10.1007/s00894-015-2656-7

Paris, Guillaume; Ramseyer, Christophe; Enescu, Mironel
A theoretical study of the unfolding pathway of reduced Human serum albumin
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 106, MAY 2015
abstract, full text, DOI:10.1007/s00894-015-2659-4

Begau, Christoph; Sutmann, Godehard
Adaptive dynamic load-balancing with irregular domain decomposition for particle simulations
COMPUTER PHYSICS COMMUNICATIONS, 190:51-61, MAY 2015
abstract, full text, DOI:10.1016/j.cpc.2015.01.009

Nakamura, Takenobu; Kawamoto, Shuhei; Shinoda, Wataru
Precise calculation of the local pressure tensor in Cartesian and spherical coordinates in LAMMPS
COMPUTER PHYSICS COMMUNICATIONS, 190:120-128, MAY 2015
abstract, full text, DOI:10.1016/j.cpc.2014.11.017

Vanommeslaeghe, K.; MacKerell, A. D., Jr.
CHARMM additive and polarizable force fields for biophysics and computer-aided drug design
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:861-871, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.08.004

Bernardi, Rafael C.; Melo, Marcelo C. R.; Schulten, Klaus
Enhanced sampling techniques in molecular dynamics simulations of biological systems
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:872-877, MAY 2015
abstract, full text, TCBG publications, DOI:10.1016/j.bbagen.2014.10.019

Batchelor, Matthew; Gowdy, James; Paci, Emanuele
Effect of external pulling forces on the length distribution of peptides
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:903-910, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.09.019

Lynch, Gillian C.; Perkyns, John S.; Bao Linh Nguyen; Pettitt, B. Montgomery
Solvation and cavity occupation in biomolecules
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:923-931, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.09.020

Cazade, Pierre-Andre; Berezovska, Ganna; Meuwly, Markus
Coupled protein-ligand dynamics in truncated hemoglobin N from atomistic simulations and transition networks
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:996-1005, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.09.008

Simonson, Thomas; Aleksandrov, Alexey; Satpati, Priyadarshi
Electrostatic free energies in translational GTPases: Classic allostery and the rest
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:1006-1016, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.07.006

Grauffel, Cedric; Stote, Roland H.; Dejaegere, Annick
Molecular dynamics for computational proteomics of methylated histone H3
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:1026-1040, MAY 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.09.015

Babcock, Jeremiah J.; Brancaleon, Lorenzo
The Effect of Local Dynamics of Atto 390-Labeled Lysozyme on Fluorescence Anisotropy Modeling
BIOPOLYMERS, 103:285-295, MAY 2015
abstract, full text, DOI:10.1002/bip.22596

Fernandez-Millan, Pablo; Lazaro, Melisa; Cansiz-Arda, Sirin; Gerhold, Joachim M.; Rajala, Nina; Schmitz, Claus-A.; Silva-Espina, Cristina; Gil, David; Bernado, Pau; Valle, Mikel; Spelbrink, Johannes N.; Sola, Maria
The hexameric structure of the human mitochondrial replicative helicase Twinkle
NUCLEIC ACIDS RESEARCH, 43:4284-4295, APR 30 2015
abstract, full text, DOI:10.1093/nar/gkv189

Pan, Xiaoliang; Schwartz, Steven D.
Free Energy Surface of the Michaelis Complex of Lactate Dehydrogenase: A Network Analysis of Microsecond Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5430-5436, APR 30 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b01840

Meneksedag-Erol, Deniz; Tang, Tian; Uudag, Hasan
Probing the Effect of miRNA on siRNA-PEI Polyplexes
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5475-5486, APR 30 2015
abstract, full text, DOI:10.1021/acs.jpcb.jb00415

Park, Min-Sun
Molecular Dynamics Simulations of the Human Glucose Transporter GLUT1
PLOS ONE, 10 Art. No. e0125361, APR 28 2015
abstract, full text, DOI:10.1371/journal.pone.0125361

Czajkowsky, Daniel M.; Andersen, Jan Terje; Fuchs, Anja; Wilson, Timothy J.; Mekhaiel, David; Colonna, Marco; He, Jianfeng; Shao, Zhifeng; Mitchell, Daniel A.; Wu, Gang; Dell, Anne; Haslam, Stuart; Lloyd, Katy A.; Moore, Shona C.; Sandlie, Inger; Blundell, Patricia A.; Pleass, Richard J.
Developing the IVIG biomimetic, Hexa-Fc, for drug and vaccine applications
SCIENTIFIC REPORTS, 5 Art. No. 9526, APR 27 2015
abstract, full text, DOI:10.1038/srep09526

Wang, Zhe; Yu, Tao; Sang, Jian-Ping; Zou, Xian-Wu; Yan, Chengfei; Zou, Xiaoqin
Computation and Simulation of the Structural Characteristics of the Kidney Urea Transporter and Behaviors of Urea Transport
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5124-5131, APR 23 2015
abstract, full text, DOI:10.1021/jp511300u

Khrenova, Maria G.; Nemukhin, Alexander V.; Domratcheva, Tatiana
Theoretical Characterization of the Flavin-Based Fluorescent Protein iLOV and its Q489K Mutant
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5176-5183, APR 23 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b01299

Esque, Jeremy; Cecchini, Marco
Accurate Calculation of Conformational Free Energy Differences in Explicit Water: The Confinement-Solvation Free Energy Approach
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5194-5207, APR 23 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b01632

Leonarski, Filip; Trylska, Joanna
RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models
BIOPHYSICAL JOURNAL, 108:1843-1847, APR 21 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.023

Weber, Daniel K.; Yao, Shenggen; Rojko, Nejc; Anderluh, Gregor; Lybrand, Terry P.; Downton, Matthew T.; Wagner, John; Separovic, Frances
Characterization of the Lipid-Binding Site of Equinatoxin II by NMR and Molecular Dynamics Simulation
BIOPHYSICAL JOURNAL, 108:1987-1996, APR 21 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.024

Procacci, Piero
Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 154117, APR 21 2015
abstract, full text, DOI:10.1063/1.4918558

Kang, Hyun-Ah; Shin, Ho-Chul; Kalantzi, Alexandra-Styliani; Toseland, Christopher P.; Kim, Hyun-Min; Gruber, Stephan; Dal Peraro, Matteo; Oh, Byung-Ha
NAR Breakthrough Article Crystal structure of Hop2-Mnd1 and mechanistic insights into its role in meiotic recombination
NUCLEIC ACIDS RESEARCH, 43:3841-3856, APR 20 2015
abstract, full text, DOI:10.1093/nar/gkv172

Thomas, Michael; Enciso, Marta; Hilder, Tamsyn A.
Insertion Mechanism and Stability of Boron Nitride Nanotubes in Lipid Bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 119:4929-4936, APR 16 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00102

Chialvo, Ariel A.; Moucka, Filip; Vlcek, Lukas; Nezbeda, Ivo
Vapor-Liquid Equilibrium and Polarization Behavior of the GCP Water Model: Gaussian Charge-on-Spring versus Dipole Self-Consistent Field Approaches to Induced Polarization
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5010-5019, APR 16 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00595

Aoun, B.; Sharma, V. K.; Pellegrini, E.; Mitra, S.; Johnson, M.; Mukhopadhyay, R.
Structure and Dynamics of Ionic Micelles: MD Simulation and Neutron Scattering Study
JOURNAL OF PHYSICAL CHEMISTRY B, 119:5079-5086, APR 16 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00020

Gouge, Jerome; Rosario, Sandrine; Romain, Felix; Poitevin, Frederic; Beguin, Pierre; Delarue, Marc
Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair
EMBO JOURNAL, 34:1126-1142, APR 15 2015
abstract, full text, DOI:10.15252/embj.201489643

Chemmama, Ilan E.; Chapagain, Prem P.; Gerstman, Bernard S.
Pairwise amino acid secondary structural propensities
PHYSICAL REVIEW E, 91 Art. No. 042709, APR 15 2015
abstract, full text, DOI:10.1103/PhysRevE.91.042709

Yuan, Yunyun; Zaidi, Saheem A.; Stevens, David L.; Scoggins, Krista L.; Mosier, Philip D.; Kellogg, Glen E.; Dewey, William L.; Selley, Dana E.; Zhang, Yan
Design, syntheses, and pharmacological characterization of 17-cyclopropylmethyl-3,14 beta-dihydroxy-4,5 alpha-epoxy-6 alpha-(isoquinoline-3 '-carboxamido)morphinan analogues as opioid receptor ligands
BIOORGANIC & MEDICINAL CHEMISTRY, 23:1701-1715, APR 15 2015
abstract, full text, DOI:10.1016/j.bmc.2015.02.055

Bennion, Brian J.; Essiz, Sebnem G.; Lau, Edmond Y.; Fattebert, Jean-Luc; Emigh, Aiyana; Lightstone, Felice C.
A Wrench in the Works of Human Acetylcholinesterase: Soman Induced Conformational Changes Revealed by Molecular Dynamics Simulations
PLOS ONE, 10 Art. No. UNSP e0121092, APR 13 2015
abstract, full text, DOI:10.1371/journal.pone.0121092

Wang, Beibei; Weng, Jingwei; Wang, Wenning
Substrate binding accelerates the conformational transitions and substrate dissociation in multidrug efflux transporter AcrB
FRONTIERS IN MICROBIOLOGY, 6 Art. No. UNSP 302, APR 13 2015
abstract, full text, DOI:10.3389/fmicb.2015.00302

Krammer, Eva-Maria; Giang Thi Vu; Homble, Fabrice; Prevost, Martine
Dual Mechanism of Ion Permeation through VDAC Revealed with Inorganic Phosphate Ions and Phosphate Metabolites
PLOS ONE, 10 Art. No. e0121746, APR 10 2015
abstract, full text, DOI:10.1371/journal.pone.0121746

Jang, Hyunbum; Abraham, Sherwin J.; Chavan, Tanmay S.; Hitchinson, Ben; Khavrutskii, Lyuba; Tarasova, Nadya I.; Nussinov, Ruth; Gaponenko, Vadim
Mechanisms of Membrane Binding of Small GTPase K-Ras4B Farnesylated Hypervariable Region
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:9465-9477, APR 10 2015
abstract, full text, DOI:10.1074/jbc.M114.620724

Kuttel, Michelle M.; Jackson, Graham E.; Mafata, Mpho; Ravenscroft, Neil
Capsular polysaccharide conformations in pneumococcal serotypes 19F and 19A
CARBOHYDRATE RESEARCH, 406:27-33, APR 10 2015
abstract, full text, DOI:10.1016/j.carres.2014.12.013

Preti, Delia; Baraldi, Pier Giovanni; Saponaro, Giulia; Romagnoli, Romeo; Tabrizi, Mojgan Aghazadeh; Baraldi, Stefania; Cosconati, Sandro; Bruno, Agostino; Novellino, Ettore; Vincenzi, Fabrizio; Ravani, Annalisa; Borea, Pier Andrea; Varani, Katia
Design, Synthesis, and Biological Evaluation of Novel 2-((2-4-(Substituted)phenylpiperazin-1-yl)ethyl)amino)-5 '-N-ethylcarboxamidoadenosines as Potent and Selective Agonists of the A(2A) Adenosine Receptor
JOURNAL OF MEDICINAL CHEMISTRY, 58:3253-3267, APR 9 2015
abstract, full text, DOI:10.1021/acs.jmedchem.5b00215

Semino, Rocio; Rodriguez, Javier
Molecular Dynamics Study of Ionic Liquids Complexation within beta-Cyclodextrins
JOURNAL OF PHYSICAL CHEMISTRY B, 119:4865-4872, APR 9 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00909

Denisov, Ilia G.; Grinkova, Yelena V.; Baylon, Javier L.; Tajkhorshid, Emad; Sligar, Stephen G.
Mechanism of Drug-Drug Interactions Mediated by Human Cytochrome P450 CYP3A4 Monomer
BIOCHEMISTRY, 54:2227-2239, APR 7 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00079

Michel Espinoza-Fonseca, L.; Autry, Joseph M.; Lizbeth Ramirez-Salinas, G.; Thomas, David D.
Atomic-Level Mechanisms for Phospholamban Regulation of the Calcium Pump
BIOPHYSICAL JOURNAL, 108:1697-1708, APR 7 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.004

Davis, Brittny C.; Brown, Jodian A.; Thorpe, Ian F.
Allosteric Inhibitors Have Distinct Effects, but Also Common Modes of Action, in the HCV Polymerase
BIOPHYSICAL JOURNAL, 108:1785-1795, APR 7 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.005

Miao, Yinglong; Caliman, Alisha D.; McCammon, J. Andrew
Allosteric Effects of Sodium Ion Binding on Activation of the M3 Muscarinic G-Protein-Coupled Receptor
BIOPHYSICAL JOURNAL, 108:1796-1806, APR 7 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.003

Lockhart, Christopher; Klimov, Dmitri K.
Calcium Enhances Binding of A beta Monomer to DMPC Lipid Bilayer
BIOPHYSICAL JOURNAL, 108:1807-1818, APR 7 2015
abstract, full text, DOI:10.1016/j.bpj.2015.03.001

Tsutakawa, Susan E.; Yan, Chunli; Xu, Xiaojun; Weinacht, Christopher P.; Freudenthal, Bret D.; Yang, Kun; Zhuang, Zhihao; Washington, M. Todd; Tainer, John A.; Ivanov, Ivaylo
Structurally Distinct Ubiquitin- and Sumo-Modified PCNA: Implications for Their Distinct Roles in the DNA Damage Response
STRUCTURE, 23:724-733, APR 7 2015
abstract, full text, DOI:10.1016/j.str.2015.02.008

Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro
Accuracy Assessment of the Linear Poisson-Boltzmann Equation and Reparametrization of the OBC Generalized Born Model for Nucleic Acids and Nucleic Acid-Protein Complexes
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:585-596, APR 5 2015
abstract, full text, DOI:10.1002/jcc.23832

Elmes, Matthew W.; Kaczocha, Martin; Berger, William T.; Leung, KwanNok; Ralph, Brian P.; Wang, Liqun; Sweeney, Joseph M.; Miyauchi, Jeremy T.; Tsirka, Stella E.; Ojima, Iwao; Deutsch, Dale G.
Fatty Acid-binding Proteins (FABPs) Are Intracellular Carriers for Delta(9)-Tetrahydrocannabinol (THC) and Cannabidiol (CBD)
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:8711-8721, APR 3 2015
abstract, full text, DOI:10.1074/jbc.M114.618447

Gillet, Jean-Numa
Ultrafast molecular dynamics of biofuel extraction for microalgae and bacteria milking: blocking membrane folding pathways to damaged lipid-bilayer conformations with nanomicelles
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:690-705, APR 3 2015
abstract, full text, DOI:10.1080/07391102.2014.907544

Jimenez, Veronica A.; Alderete, Joel B.; Navarrete, Karen R.
Structural insight into epothilones antitumor activity based on the conformational preferences and tubulin binding modes of epothilones A and B obtained from molecular dynamics simulations
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:789-803, APR 3 2015
abstract, full text, DOI:10.1080/07391102.2014.911702

Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith; Liu, Bo; Bernardi, Rafael C.; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus
Molecular dynamics simulations of large macromolecular complexes
CURRENT OPINION IN STRUCTURAL BIOLOGY, 31:64-74, APR 2015
abstract, full text, TCBG publications, DOI:10.1016/j.sbi.2015.03.007

Tian, Jian; Woodard, Jaie C.; Whitney, Anna; Shakhnovich, Eugene I.
Thermal Stabilization of Dihydrofolate Reductase Using Monte Carlo Unfolding Simulations and Its Functional Consequences
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004207, APR 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004207

Rismanian, M.; Saidi, M. S.; Firoozabadi, B.
Na+ permeation through its protein channels, from molecular dynamics to continuum modeling
SCIENTIA IRANICA, 22:459-466, APR 2015
abstract, full text

Tan, Pengli; Feng, Zhiwei; Zhang, Liling; Hou, Tingjun; Li, Youyong
The mechanism of proton translocation in respiratory complex I from molecular dynamics
JOURNAL OF RECEPTORS AND SIGNAL TRANSDUCTION, 35:170-179, APR 2015
abstract, full text, DOI:10.3109/10799893.2014.942464

Bae, Euiyoung; Moon, Sojin; Phillips, George N., Jr.
Molecular dynamics simulation of a psychrophilic adenylate kinase
JOURNAL OF THE KOREAN SOCIETY FOR APPLIED BIOLOGICAL CHEMISTRY, 58:209-212, APR 2015
abstract, full text, DOI:10.1007/s13765-015-0033-y

Lee, Myeongsang; Chang, Hyun Joon; Kim, Donghoi; Lee, Yongwoo; Suh, Heesu; Ahn, Namjo; Yoon, Gwonchan; Na, Sungsoo
Relationship between structural composition and material properties of polymorphic hIAPP fibrils
BIOPHYSICAL CHEMISTRY, 199:1-8, APR 2015
abstract, full text, DOI:10.1016/j.bpc.2015.02.002

Pietra, Francesco
Restoring Histone Deacetylase Activity by Waste Product Release. A View from Molecular Mechanics Simulations with Mammalian HDAC8
CHEMISTRY & BIODIVERSITY, 12:503-512, APR 2015
abstract, full text, DOI:10.1002/cbdv.201400314

Wan, Hua; Chang, Shan; Hu, Jian-ping; Tian, Yuan-xin; Tian, Xu-hong
Molecular Dynamics Simulations of Ternary Complexes: Comparisons of LEAFY Protein Binding to Different DNA Motifs
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:784-794, APR 2015
abstract, full text, DOI:10.1021/ci500705j

Belmonte, Luca; Moran, Oscar
On the interactions between nucleotide binding domains and membrane spanning domains in cystic fibrosis transmembrane regulator: A molecular dynamic study
BIOCHIMIE, 111:19-29, APR 2015
abstract, full text, DOI:10.1016/j.biochi.2015.01.010

Myklebust, Line M.; Van Damme, Petra; Stove, Svein I.; Doerfel, Max J.; Abboud, Angele; Kalvik, Thomas V.; Grauffel, Cedric; Jonckheere, Veronique; Wu, Yiyang; Swensen, Jeffrey; Kaasa, Hanna; Liszczak, Glen; Marmorstein, Ronen; Reuter, Nathalie; Lyon, Gholson J.; Gevaert, Kris; Arnesen, Thomas
Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects
HUMAN MOLECULAR GENETICS, 24:1956-1976, APR 1 2015
abstract, full text, DOI:10.1093/hmg/ddu611

Bao Linh Nguyen; Pettitt, B. Montgomery
Effects of Acids, Bases, and Heteroatoms on Proximal Radial Distribution Functions for Proteins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:1399-1409, APR 2015
abstract, full text, DOI:10.1021/ct501116v

Chen, Liao Y.
Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand-Protein Complexes: A Brute Force Approach That Is Fast and Accurate
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:1928-1938, APR 2015
abstract, full text, DOI:10.1021/ct501162f

Lehman, William; Medlock, Greg; Li, Xiaochuan (Edward); Suphamungmee, Worawit; Tu, An-Yue; Schmidtmann, Anja; Ujfalusi, Zoltan; Fischer, Stefan; Moore, Jeffrey R.; Geeves, Michael A.; Regnier, Michael
Phosphorylation of Ser283 enhances the stiffness of the tropomyosin head-to-tail overlap domain
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 571:10-15, APR 1 2015
abstract, full text, DOI:10.1016/j.abb.2015.02.026

Mitra, Suranjita; Mukhopadhyay, Bidhan Chandra; Mandal, Anisur Rahaman; Arukha, Ananta Prasad; Chakrabarty, Kuheli; Das, Gourab Kanti; Chakrabartty, Pran Krishna; Biswas, Swadesh Ranjan
Cloning, overexpression, and characterization of a novel alkali-thermostable xylanase from Geobacillus sp WBI
JOURNAL OF BASIC MICROBIOLOGY, 55:527-537, APR 2015
abstract, full text, DOI:10.1002/jobm.201400495

Tarasevich, Barbara J.; Philo, John S.; Maluf, Nasib Karl; Krueger, Susan; Buchko, Garry W.; Lin, Genyao; Shaw, Wendy J.
The leucine-rich amelogenin protein (LRAP) is primarily monomeric and unstructured in physiological solution
JOURNAL OF STRUCTURAL BIOLOGY, 190:81-91, APR 2015
abstract, full text, DOI:10.1016/j.jsb.2014.10.007

Pedretti, Alessandro; Mazzolari, Angelica; Ricci, Chiara; Vistoli, Giulio
Enhancing the Reliability of GPCR Models by Accounting for Flexibility of Their Pro-Containing Helices: the Case of the Human mAChR1 Receptor
MOLECULAR INFORMATICS, 34:216-227, APR 2015
abstract, full text, DOI:10.1002/minf.201400159

Kaczor, Agnieszka A.; Guixa-Gonzalez, Ramon; Carrio, Pau; Poso, Antti; Dove, Stefan; Pastor, Manuel; Selent, Jana
Multi-Component Protein - Protein Docking Based Protocol with External Scoring for Modeling Dimers of G Protein-Coupled Receptors
MOLECULAR INFORMATICS, 34:246-255, APR 2015
abstract, full text, DOI:10.1002/minf.201400088

Jorgensen, Christian; Darre, Leonardo; Vanommeslaeghe, Kenno; Omoto, Kiyoyuki; Pryde, David; Domene, Carmen
In Silico Identification of PAP-1 Binding Sites in the Kv1.2 Potassium Channel
MOLECULAR PHARMACEUTICS, 12:1299-1307, APR 2015
abstract, full text, DOI:10.1021/acs.molpharmaceut.5b00023

Wang, Zhiming; Qiao, Zhu; Ye, Sheng; Zhang, Rongguang
Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 71:779-789, APR 2015
abstract, full text, DOI:10.1107/S1399004715001169

Johnson, Jennifer L.; Entzminger, Kevin C.; Hyun, Jeongmin; Kalyoncu, Sibel; Heaner, David P., Jr.; Morales, Ivan A.; Sheppard, Aly; Gumbart, James C.; Maynard, Jennifer A.; Lieberman, Raquel L.
Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 71:896-906, APR 2015
abstract, full text, DOI:10.1107/S1399004715001856

Comitani, Federico; Melis, Claudio; Molteni, Carla
Elucidating ligand binding and channel gating mechanisms in pentameric ligand-gated ion channels by atomistic simulations
BIOCHEMICAL SOCIETY TRANSACTIONS, 43:151-156, APR 2015
abstract, full text, DOI:10.1042/BST20140259

Montanez, Mara I.; Najera, Francisco; Mayorga, Cristobalina; Ruiz-Sanchez, Antonio J.; Vida, Yolanda; Collado, Daniel; Blanca, Miguel; Torres, Maria J.; Perez-Inestrosa, Ezequiel
Recognition of multiepitope dendrimeric antigens by human immunoglobulin E
NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE, 11:579-588, APR 2015
abstract, full text, DOI:10.1016/j.nano.2015.01.006

Dokainish, Hisham M.; Gauld, James W.
Formation of a Stable Iminol Intermediate in the Redox Regulation Mechanism of Protein Tyrosine Phosphatase 1B (PTP1B)
ACS CATALYSIS, 5:2195-2202, APR 2015
abstract, full text, DOI:10.1021/cs501707h

Kwon, Tae Woo; Ambrosia, Matthew Stanley; Jang, Joonkyoung; Ha, Man Yeong
Dynamic hydrophobicity of heterogeneous pillared surfaces at the nano-scale
JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY, 29:1663-1671, APR 2015
abstract, full text, DOI:10.1007/s12206-015-0338-0

Nguyen, Phuong T. V.; Yu, Haibo; Keller, Paul A.
Identification of chikungunya virus nsP2 protease inhibitors using structure-base approaches
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 57:1-8, APR 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.01.001

Azamat, Jafar; Khataee, Alireza; Joo, Sang Woo; Yin, Binfeng
Removal of trihalomethanes from aqueous solution through armchair carbon nanotubes: A molecular dynamics study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 57:70-75, APR 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.01.008

Behera, Pabitra Mohan; Behera, Deepak Kumar; Satpati, Suresh; Agnihotri, Geetanjali; Nayak, Sanghamitra; Padhi, Payodhar; Dixit, Anshuman
Molecular modeling and identification of novel glucokinase activators through stepwise virtual screening
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 57:122-130, APR 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.01.012

Viricel, Clement; Ahmed, Marawan; Barakat, Khaled
Human PD-1 binds differently to its human ligands: A comprehensive modeling study
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 57:131-142, APR 2015
abstract, full text, DOI:10.1016/j.jmgm.2015.01.015

Dong, Sijia S.; Abrol, Ravinder; Goddard, William A.
The Predicted Ensemble of Low-Energy Conformations of Human Somatostatin Receptor Subtype 5 and the Binding of Antagonists
CHEMMEDCHEM, 10:650-661, APR 2015
abstract, full text, DOI:10.1002/cmdc.201500023

Aitha, Mahesh; Moritz, Lindsay; Sahu, Indra D.; Sanyurah, Omar; Roche, Zahilyn; McCarrick, Robert; Lorigan, Gary A.; Bennett, Brian; Crowder, Michael W.
Conformational dynamics of metallo-beta-lactamase CcrA during catalysis investigated by using DEER spectroscopy
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 20:585-594, APR 2015
abstract, full text, DOI:10.1007/s00775-015-1244-8

D'Avino, Gabriele; Muccioli, Luca; Zannoni, Claudio
From Chiral Islands to Smectic Layers: A Computational Journey Across Sexithiophene Morphologies on C-60
ADVANCED FUNCTIONAL MATERIALS, 25:1985-1995, APR 1 2015
abstract, full text, DOI:10.1002/adfm.201402609

Sfyroera, Georgia; Ricklin, Daniel; Reis, Edimara S.; Chen, Hui; Wu, Emilia L.; Kaznessis, Yiannis N.; Ekdahl, Kristina N.; Nilsson, Bo; Lambris, John D.
Rare Loss-of-Function Mutation in Complement Component C3 Provides Insight into Molecular and Pathophysiological Determinants of Complement Activity
JOURNAL OF IMMUNOLOGY, 194:3305-3316, APR 1 2015
abstract, full text, DOI:10.4049/jimmunol.1402781

Qu, Tao; Verma, Devendra; Shahidi, Mehran; Pichler, Bernhard; Hellmich, Christian; Tomar, Vikas
Mechanics of organic-inorganic biointerfaces-Implications for strength and creep properties
MRS BULLETIN, 40:349-358, APR 2015
abstract, full text, DOI:10.1557/mrs.2015.70

Mernea, Maria; Ionescu, Alina; Vasile, Ionut; Nica, Cristina; Stoian, Gheorghe; Dascalu, Traian; Mihailescu, Dan Florin
In vitro human serum albumin glycation monitored by Terahertz spectroscopy
OPTICAL AND QUANTUM ELECTRONICS, 47:961-973, APR 2015
abstract, full text, DOI:10.1007/s11082-015-0129-y

Mornon, Jean-Paul; Hoffmann, Brice; Jonic, Slavica; Lehn, Pierre; Callebaut, Isabelle
Full-open and closed CFTR channels, with lateral tunnels from the cytoplasm and an alternative position of the F508 region, as revealed by molecular dynamics
CELLULAR AND MOLECULAR LIFE SCIENCES, 72:1377-1403, APR 2015
abstract, full text, DOI:10.1007/s00018-014-1749-2

Alaybeyoglu, Begum; Sariyar Akbulut, Berna; Ozkirimli, Elif
A novel chimeric peptide with antimicrobial activity
JOURNAL OF PEPTIDE SCIENCE, 21:294-301, APR 2015
abstract, full text, DOI:10.1002/psc.2739

Zhang, Peng; Deng, Yuefan; Feng, Rui; Luo, Xingguo; Wu, Jiangxing
Evaluation of Various Networks Configurated by Adding Bypass or Torus Links
IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS, 26:984-996, APR 2015
abstract, full text, DOI:10.1109/TPDS.2014.2315201

Sharma, Anurag; Payne, Scott; Katti, Kalpana S.; Katti, Dinesh R.
Evaluating Molecular Interactions in Polycaprolactone-Biomineralized Hydroxyapatite Nanocomposites using Steered Molecular Dynamics
JOM, 67:733-743, APR 2015
abstract, full text, DOI:10.1007/s11837-015-1361-4

Zhang, Pu-pu; Zhao, Li; Long, Shi-yang; Tian, Pu
The effect of ligands on the thermal stability of sulfotransferases: a molecular dynamics simulation study
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 72, APR 2015
abstract, full text, DOI:10.1007/s00894-015-2625-1

Sensoy, Ozge; Weinstein, Hare
A mechanistic role of Helix 8 in GPCRs: Computational modeling of the dopamine D2 receptor interaction with the GIPC1-PDZ-domain
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:976-983, APR 2015
abstract, full text, DOI:10.1016/j.bbamem.2014.12.002

Rogers, David M.; Kent, Michael S.; Rempe, Susan B.
Molecular basis of endosomal-membrane association for the dengue virus envelope protein
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:1041-1052, APR 2015
abstract, full text, DOI:10.1016/j.bbamem.2014.12.018

Trung Dac Nguyen; Plimpton, Steven J.
Accelerating dissipative particle dynamics simulations for soft matter systems
COMPUTATIONAL MATERIALS SCIENCE, 100:173-180, APR 1 2015
abstract, full text, DOI:10.1016/j.commatsci.2014.10.068

Feroz, Shevin R.; Teoh, Yue Jun; Mohamad, Saharuddin B.; Hong, Sok Lai; Malek, Sri Na.; Tayyab, Saad
Interaction of flavokawain B with lysozyme: A photophysical and molecular simulation study
JOURNAL OF LUMINESCENCE, 160:101-109, APR 2015
abstract, full text, DOI:10.1016/j.jlumin.2014.11.053

Garcia, Pamela Soto; Dario Moreau, Alberto Luis; Magalhaes Ierich, Jessica Cristiane; Araujo Vig, Ana Carolina; Higa, Akemi Martins; Oliveira, Guedmiller S.; Abdalla, Fabio Camargo; Hausen, Moema; Leite, Fabio L.
A Nanobiosensor Based on 4-Hydroxyphenylpyruvate Dioxygenase Enzyme for Mesotrione Detection
IEEE SENSORS JOURNAL, 15:2106-2113, APR 2015
abstract, full text, DOI:10.1109/JSEN.2014.2371773

Vermaas, Josh V.; Taguchi, Alexander T.; Dikanov, Sergei A.; Wraight, Colin A.; Tajkhorshid, Emad
Redox Potential Tuning through Differential Quinone Binding in the Photosynthetic Reaction Center of Rhodobacter sphaeroides
BIOCHEMISTRY, 54:2104-2116, MAR 31 2015
abstract, full text, DOI:10.1021/acs.biochem.5b00033

Chandramouli, Balasubramanian; Di Maio, Danilo; Mancini, Giordano; Barone, Vincenzo; Brancato, Giuseppe
Breaking the Hydrophobicity of the MscL Pore: Insights into a Charge-Induced Gating Mechanism
PLOS ONE, 10 Art. No. e0120196, MAR 31 2015
abstract, full text, DOI:10.1371/journal.pone.0120196

Ho, Jianghai; Perez-Aguilar, Jose Manuel; Gao, Lu; Saven, Jeffery G.; Matsunami, Hiroaki; Eckenhoff, Roderic G.
Molecular recognition of ketamine by a subset of olfactory G protein-coupled receptors
SCIENCE SIGNALING, 8 Art. No. ra33, MAR 31 2015
abstract, full text, DOI:10.1126/scisignal.2005912

Lai, Pin-Kuang; Lin, Shiang-Tai
Internal Coordinate Density of State from Molecular Dynamics Simulation
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:507-517, MAR 30 2015
abstract, full text, DOI:10.1002/jcc.23822

Padhi, Siladitya; Ramakrishna, Siddabattula; Priyakumar, U. Deva
Prediction of the Structures of Helical Membrane Proteins Based on a Minimum Unfavorable Contacts Approach
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:539-552, MAR 30 2015
abstract, full text, DOI:10.1002/jcc.23828

Martinez, Leandro
Automatic Identification of Mobile and Rigid Substructures in Molecular Dynamics Simulations and Fractional Structural Fluctuation Analysis
PLOS ONE, 10 Art. No. e0119264, MAR 27 2015
abstract, full text, DOI:10.1371/journal.pone.0119264

Loerbroks, Claudia; Boulanger, Eliot; Thiel, Walter
Solvent Influence on Cellulose 1,4-beta-Glycosidic Bond Cleavage: A Molecular Dynamics and Metadynarnics Study
CHEMISTRY-A EUROPEAN JOURNAL, 21:5477-5487, MAR 27 2015
abstract, full text, DOI:10.1002/chem.201405507

Sanchez-Rodriguez, Jorge E.; Khalili-Araghi, Fatemeh; Miranda, Pablo; Roux, Benoit; Holmgren, Miguel; Bezanilla, Francisco
A Structural Rearrangement of the Na+/K+-ATPase Traps Ouabain within the External Ion Permeation Pathway
JOURNAL OF MOLECULAR BIOLOGY, 427:1335-1344, MAR 27 2015
abstract, full text, DOI:10.1016/j.jmb.2015.01.011

Girdhar, Anuj; Sathe, Chaitanya; Schulten, Klaus; Leburton, Jean-Pierre
Tunable graphene quantum point contact transistor for DNA detection and characterization
NANOTECHNOLOGY, 26 Art. No. 134005, MAR 27 2015
abstract, full text, TCBG publications, DOI:10.1088/0957-4484/26/13/134005

Savelyev, Alexey; MacKerell, Alexander D., Jr.
Competition among Li+, Na+, K+, and Rb+ Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields
JOURNAL OF PHYSICAL CHEMISTRY B, 119:4428-4440, MAR 26 2015
abstract, full text, DOI:10.1021/acs.jpcb.5b00683

Rheault, Jean-Francois; Gagne, Eve; Guertin, Michel; Lamoureux, Guillaume; Auger, Michele; Laguee, Patrick
Molecular Model of Hemoglobin N from Mycobacterium tuberculosis Bound to Lipid Bilayers: A Combined Spectroscopic and Computational Study
BIOCHEMISTRY, 54:2073-2084, MAR 24 2015
abstract, full text, DOI:10.1021/bi5010624

Guo, Jiqing; Cheng, Yen May; Lees-Miller, James P.; Perissinotti, Laura L.; Claydon, Tom W.; Hull, Christina M.; Thouta, Samrat; Roach, Daniel E.; Durdagi, Serdar; Noskov, Sergei Y.; Duff, Henry J.
NS1643 Interacts around L529 of hERG to Alter Voltage Sensor Movement on the Path to Activation
BIOPHYSICAL JOURNAL, 108:1400-1413, MAR 24 2015
abstract, full text, DOI:10.1016/j.bpj.2014.12.055

Morgan, Brittany R.; Deveau, Laura M.; Massi, Francesca
Probing the Structural and Dynamical Effects of the Charged Residues of the TZF Domain of TIS11d
BIOPHYSICAL JOURNAL, 108:1503-1515, MAR 24 2015
abstract, full text, DOI:10.1016/j.bpj.2015.01.039

Burmann, Bjoern M.; Holdbrook, Daniel A.; Callon, Morgane; Bond, Peter J.; Hiller, Sebastian
Revisiting the Interaction between the Chaperone Skp and Lipopolysaccharide
BIOPHYSICAL JOURNAL, 108:1516-1526, MAR 24 2015
abstract, full text, DOI:10.1016/j.bpj.2015.01.029

Plascencia-Villa, German; Torrente, Daniel; Marucho, Marcelo; Jose-Yacaman, Miguel
Biodirected Synthesis and Nanostructural Characterization of Anisotropic Gold Nanoparticles
LANGMUIR, 31:3527-3536, MAR 24 2015
abstract, full text, DOI:10.1021/acs.langmuir.5b00084

Ren, Baiping; Gao, Huipeng; Cao, Yafeng; Jia, Lingyun
In Silico understanding of the cyclodextrin-phenanthrene hybrid assemblies in both aqueous medium and bacterial membranes
JOURNAL OF HAZARDOUS MATERIALS, 285:148-156, MAR 21 2015
abstract, full text, DOI:10.1016/j.jhazmat.2014.12.001

Zhang, Xing; Lei, Dongsheng; Zhang, Lei; Rames, Matthew; Zhang, Shengli
A Model of Lipid-Free Apolipoprotein A-I Revealed by Iterative Molecular Dynamics Simulation
PLOS ONE, 10 Art. No. e0120233, MAR 20 2015
abstract, full text, DOI:10.1371/journal.pone.0120233

Andrijchenko, Natalya N.; Ermilov, Alexander Yu.; Khriachtchev, Leonid; Rasanen, Markku; Nemukhin, Alexander V.
Toward Molecular Mechanism of Xenon Anesthesia: A Link to Studies of Xenon Complexes with Small Aromatic Molecules
JOURNAL OF PHYSICAL CHEMISTRY A, 119:2517-2521, MAR 19 2015
abstract, full text, DOI:10.1021/jp508800k

Shilov, Ignat Yu.
Molecular dynamics simulation of dielectric constant and cluster structure of liquid methanol: the role of cluster-cluster dipole correlations
MOLECULAR PHYSICS, 113:570-576, MAR 19 2015
abstract, full text, DOI:10.1080/00268976.2014.960496

Mehta, Jatin; Asthana, Shailendra; Mandal, Chandi Charan; Saxena, Sunita
A Molecular Analysis Provides Novel Insights into Androgen Receptor Signalling in Breast Cancer
PLOS ONE, 10 Art. No. e0120622, MAR 17 2015
abstract, full text, DOI:10.1371/journal.pone.0120622

Blair, Jessica M. A.; Bavro, Vassiliy N.; Ricci, Vito; Modi, Niraj; Cacciotto, Pierpaolo; Kleinekathoefer, Ulrich; Ruggerone, Paolo; Vargiu, Attilio V.; Baylay, Alison J.; Smith, Helen E.; Brandon, Yvonne; Galloway, David; Piddock, Laura J. V.
AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:3511-3516, MAR 17 2015
abstract, full text, DOI:10.1073/pnas.1419939112

Kinoshita, Mikitaka; Okada, Tetsuji
Structural conservation among the rhodopsin-like and other G protein-coupled receptors
SCIENTIFIC REPORTS, 5 Art. No. 9176, MAR 17 2015
abstract, full text, DOI:10.1038/srep09176

Bruno, Agostino; Scrima, Mario; Novellino, Ettore; D'Errico, Gerardino; D'Ursi, Anna Maria; Limongelli, Vittorio
The Glycan Role in the Glycopeptide Immunogenicity Revealed by Atomistic Simulations and Spectroscopic Experiments on the Multiple Sclerosis Biomarker CSF114(Glc)
SCIENTIFIC REPORTS, 5 Art. No. 9200, MAR 17 2015
abstract, full text, DOI:10.1038/srep09200

Mizuguchi, Tomoko; Ishizuka, Ryosuke; Matubayasi, Nobuyuki
Effect of diffuseness of micelle boundary on the solute distribution upon solubilization
CHEMICAL PHYSICS LETTERS, 624:19-23, MAR 16 2015
abstract, full text, DOI:10.1016/j.cplett.2015.02.001

Hameau, Aurelien; Fruchon, Severine; Bijani, Christian; Barducci, Alessandro; Blanzat, Muriel; Poupot, Remy; Pavan, Giovanni M.; Caminade, Anne-Marie; Turrin, Cedric-Olivier
Theoretical and Experimental Characterization of Amino-PEG-Phosphonate-Terminated Polyphosphorhydrazone Dendrimers: Influence of Size and PEG Capping on Cytotoxicity Profiles
JOURNAL OF POLYMER SCIENCE PART A-POLYMER CHEMISTRY, 53:761-774, MAR 15 2015
abstract, full text, DOI:10.1002/pola.27501

Hanasaki, Itsuo; Nagura, Ryo; Kawano, Satoyuki
Coarse-grained picture of Brownian motion in water: Role of size and interaction distance range on the nature of randomness
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 104301, MAR 14 2015
abstract, full text, DOI:10.1063/1.4913748

Megow, Joerg; Roehr, Merle I. S.; Busch, Marcel Schmidt am; Renger, Thomas; Mitric, Roland; Kirstein, Stefan; Rabe, Juergen P.; May, Volkhard
Site-dependence of van der Waals interaction explains exciton spectra of double-walled tubular J-aggregates
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:6741-6747, MAR 14 2015
abstract, full text, DOI:10.1039/c4cp05945j

Liu, Yingzhe; Lai, Weipeng; Yu, Tao; Kang, Ying; Ge, Zhongxue
Interactions of carbon nanotubes with the nitromethane-water mixture governing selective adsorption of energetic molecules from aqueous solution
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:6995-7001, MAR 14 2015
abstract, full text, DOI:10.1039/c4cp05909c

Hu, Yunfei; Wu, Yujie; Li, Qianwen; Zhang, Wenbo; Jin, Changwen
Solution Structure of Yeast Rpn9 INSIGHTS INTO PROTEASOME LID ASSEMBLY
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:6878-6889, MAR 13 2015
abstract, full text, DOI:10.1074/jbc.M114.626762

Islam, Shahidul M.; Roux, Benoit
Simulating the Distance Distribution between Spin-Labels Attached to Proteins
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3901-3911, MAR 12 2015
abstract, full text, DOI:10.1021/jp510745d

Lee, Cheng-Kuang; Pao, Chun-Wei; Smit, Berend
PSII-LHCII Supercomplex Organizations in Photosynthetic Membrane by Coarse-Grained Simulation
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3999-4008, MAR 12 2015
abstract, full text, DOI:10.1021/jp511277c

Dubiez, Etienne; Aleksandrov, Alexey; Lazennec-Schurdevin, Christine; Mechulam, Yves; Schmitt, Emmanuelle
Identification of a second GTP-bound magnesium ion in archaeal initiation factor 2
NUCLEIC ACIDS RESEARCH, 43:2946-2957, MAR 11 2015
abstract, full text, DOI:10.1093/nar/gkv053

Serratos, Iris N.; Castellanos, Pilar; Pastor, Nina; Millan-Pacheco, Cesar; Rembao, Daniel; Perez-Montfort, Ruy; Cabrera, Nallely; Reyes-Espinosa, Francisco; Diaz-Garrido, Paulina; Lopez-Macay, Ambar; Martinez-Flores, Karina; Lopez-Reyes, Alberto; Sanchez-Garcia, Aurora; Cuevas, Elvis; Santamaria, Abel
Modeling the Interaction between Quinolinate and the Receptor for Advanced Glycation End Products (RAGE): Relevance for Early Neuropathological Processes
PLOS ONE, 10 Art. No. UNSP e0120221, MAR 10 2015
abstract, full text, DOI:10.1371/journal.pone.0120221

Chen, Qi; Luan, Zheng-Jiao; Cheng, Xiaolin; Xu, Jian-He
Molecular Dynamics Investigation of the Substrate Binding Mechanism in Carboxylesterase
BIOCHEMISTRY, 54:1841-1848, MAR 10 2015
abstract, full text, DOI:10.1021/bi5015612

Leone, Vanessa; Pogoryelov, Denys; Meier, Thomas; Faraldo-Gomez, Jose D.
On the principle of ion selectivity in Na+/H+-coupled membrane proteins: Experimental and theoretical studies of an ATP synthase rotor
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E1057-E1066, MAR 10 2015
abstract, full text, DOI:10.1073/pnas.1421202112

Lee, Hui Sun; Qi, Yifei; Im, Wonpil
Effects of N-glycosylation on protein conformation and dynamics: Protein Data Bank analysis and molecular dynamics simulation study
SCIENTIFIC REPORTS, 5 Art. No. 8926, MAR 9 2015
abstract, full text, DOI:10.1038/srep08926

Carr, Matthew; MacPhee, Cait E.
Membrainy: a 'smart', unified membrane analysis tool
SOURCE CODE FOR BIOLOGY AND MEDICINE, 10 Art. No. 3, MAR 7 2015
abstract, full text, DOI:10.1186/s13029-015-0033-7

Mendoza-Martinez, Cesar; Galindo-Sevilla, Norma; Correa-Basurto, Jose; Manuel Ugalde-Saldivar, Victor; Georgina Rodriguez-Delgado, Rosa; Hernandez-Pineda, Jessica; Padierna-Mota, Cecilia; Flores-Alamo, Marcos; Hernandez-Luis, Francisco
Antileishmanial activity of quinazoline derivatives: Synthesis, docking screens, molecular dynamic simulations and electrochemical studies
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 92:314-331, MAR 6 2015
abstract, full text, DOI:10.1016/j.ejmech.2014.12.051

Yamamoto, Eiji; Akimoto, Takuma; Yasui, Masato; Yasuoka, Kenji
Origin of 1/f noise in hydration dynamics on lipid membrane surfaces
SCIENTIFIC REPORTS, 5 Art. No. 8876, MAR 6 2015
abstract, full text, DOI:10.1038/srep08876

Weng, Jingwei; Yang, Yanhong; Wang, Wenning
Lipid Regulated Conformational Dynamics of the Longin SNARE Protein Ykt6 Revealed by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 119:1554-1562, MAR 5 2015
abstract, full text, DOI:10.1021/jp5075708

Guzman, Irisbel; Ghaemi, Zhaleh; Baranger, Anne; Luthey-Schulten, Zaida; Gruebele, Martin
Native Conformational Dynamics of the Spliceosomal U1A Protein
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3651-3661, MAR 5 2015
abstract, full text, DOI:10.1021/jp511760m

Zenn, Roland K.; Abad, Enrique; Kaestner, Johannes
Influence of the Environment on the Oxidative Deamination of p-Substituted Benzylamines in Monoamine Oxidase
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3678-3686, MAR 5 2015
abstract, full text, DOI:10.1021/jp512470a

Nierzwicki, Lukasz; Czub, Jacek
Specific Binding of Cholesterol to the Amyloid Precursor Protein: Structure of the Complex and Driving Forces Characterized in Molecular Detail
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:784-790, MAR 5 2015
abstract, full text, DOI:10.1021/acs.jpclett.5b00197

Miyashita, Naoyuki; Re, Suyong; Sugita, Yuji
REIN: Replica-Exchange INterface for Simulating Protein Dynamics and Function
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 115:325-332, MAR 5 2015
abstract, full text, DOI:10.1002/qua.24785

Yoshii, Noriyuki; Andoh, Yoshimichi; Fujimoto, Kazushi; Kojima, Hidekazu; Yamada, Atsushi; Okazaki, Susumu
MODYLAS: A Highly Parallelized General-Purpose Molecular Dynamics Simulation Program
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 115:342-348, MAR 5 2015
abstract, full text, DOI:10.1002/qua.24841

Ma, Wen; Schulten, Klaus
Mechanism of Substrate Trans location by a Ring-Shaped ATPase Motor at Millisecond Resolution
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:3031-3040, MAR 4 2015
abstract, full text, TCBG publications, DOI:10.1021/ja512605w

Yu, Tang-Qing; Lapelosa, Mauro; Vanden-Eijnden, Eric; Abrams, Cameron F.
Full Kinetics of CO Entry, Internal Diffusion, and Exit in Myoglobin from Transition-Path Theory Simulations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:3041-3050, MAR 4 2015
abstract, full text, DOI:10.1021/ja512484q

Zhang, Meng; Charles, River; Tong, Huimin; Zhang, Lei; Patel, Mili; Wang, Francis; Rames, Matthew J.; Ren, Amy; Rye, Kerry-Anne; Qiu, Xiayang; Johns, Douglas G.; Charles, M. Arthur; Ren, Gang
HDL surface lipids mediate CETP binding as revealed by electron microscopy and molecular dynamics simulation
SCIENTIFIC REPORTS, 5 Art. No. 8741, MAR 4 2015
abstract, full text, DOI:10.1038/srep08741

Yao, Huili; Rui, Huan; Kumar, Ritesh; Eshelman, Kate; Lovell, Scott; Battaile, Kevin P.; Im, Wonpil; Rivera, Mario
Concerted Motions Networking Pores and Distant Ferroxidase Centers Enable Bacterioferritin Function and Iron Traffic
BIOCHEMISTRY, 54:1611-1627, MAR 3 2015
abstract, full text, DOI:10.1021/bi501255r

Fetics, Susan K.; Guterres, Hugo; Kearney, Bradley M.; Buhrman, Greg; Ma, Buyong; Nussinov, Ruth; Mattos, Carla
Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD
STRUCTURE, 23:505-516, MAR 3 2015
abstract, full text, DOI:10.1016/j.str.2014.12.017

Vashisth, Harish
Theoretical and Computational Studies of Peptides and Receptors of the Insulin Family
MEMBRANES, 5:48-83, MAR 2015
abstract, full text, DOI:10.3390/membranes5010048

Pankavich, Stephen; Ortoleva, Peter
A Review of Two Multiscale Methods for the Simulation of Macromolecular Assemblies: Multiscale Perturbation and Multiscale Factorization
COMPUTATION, 3:29-57, MAR 2015
abstract, full text, DOI:10.3390/computation3010029

Merzhievskii, L. A.
Deformation models under intense dynamic loading (Review)
COMBUSTION EXPLOSION AND SHOCK WAVES, 51:269-283, MAR 2015
abstract, full text, DOI:10.1134/S0010508215020100

Ganesan, Prabhakar; Kim, Jong Goo; Lee, Jae Hyuk; Kim, Jeongho; Ihee, Hyotcherl
Implicit vs. Explicit Solvent Models for Calculating X-ray Solution Scattering Curves
BULLETIN OF THE KOREAN CHEMICAL SOCIETY, 36:955-962, MAR 2015
abstract, full text, DOI:10.1002/bkcs.10178

Yuan, Li; Nerngchamnong, Nisachol; Cao, Liang; Hamoudi, Hicham; del Barco, Enrique; Roemer, Max; Sriramula, Ravi K.; Thompson, Damien; Nijhuis, Christian A.
Controlling the direction of rectification in a molecular diode
NATURE COMMUNICATIONS, 6 Art. No. 6324, MAR 2015
abstract, full text, DOI:10.1038/ncomms7324

Schiro, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Haertlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin
Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins
NATURE COMMUNICATIONS, 6 Art. No. 6490, MAR 2015
abstract, full text, DOI:10.1038/ncomms7490

Miguel, Amanda; Hsin, Jen; Liu, Tianyun; Tang, Grace; Altman, Russ B.; Huang, Kerwyn Casey
Variations in the Binding Pocket of an Inhibitor of the Bacterial Division Protein FtsZ across Genotypes and Species
PLOS COMPUTATIONAL BIOLOGY, 11 Art. No. e1004117, MAR 2015
abstract, full text, DOI:10.1371/journal.pcbi.1004117

Duran-Lara, Esteban F.; Avila-Salas, Fabian; Galaz, Sebastian; John, Amalraj; Marican, Adolfo; Gutierrez, Margarita; Nachtigall, Fabiane M.; Gonzalez-Nilo, Fernando D.; Santos, Leonardo S.
Nano-Detoxification of Organophosphate Agents by PAMAM Derivatives
JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY, 26:580-591, MAR 2015
abstract, full text, DOI:10.5935/0103-5053.20150013

Wu, Di
Proline puckering parameters for collagen structure simulations
AIP ADVANCES, 5 Art. No. 037124, MAR 2015
abstract, full text, DOI:10.1063/1.4915295

Chen, Qi; Cheng, Xiaolin; Wei, Dongqing; Xu, Qin
Molecular Dynamics Simulation Studies of the Wild Type and E92Q/N155H Mutant of Elvitegravir-resistance HIV-1 Integrase
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 7:36-42, MAR 2015
abstract, full text, DOI:10.1007/s12539-014-0235-8

Izanloo, C.
Investigation of changes in the arrangement of water molecules and salt ions surrounding different atoms of the DNA molecule during the melting process: a molecular dynamics simulation study
CANADIAN JOURNAL OF CHEMISTRY, 93:348-361, MAR 2015
abstract, full text, DOI:10.1139/cjc-2014-0371

Feng, Zhiwei; Pearce, Larry V.; Xu, Xiaomeng; Yang, Xiaole; Yang, Peng; Blumberg, Peter M.; Xie, Xiang-Qun
Structural Insight into Tetrameric hTRPV1 from Homology Modeling, Molecular Docking, Molecular Dynamics Simulation, Virtual Screening, and Bioassay Validations
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:572-588, MAR 2015
abstract, full text, DOI:10.1021/ci5007189

Tsigelny, Igor F.; Sharikov, Yuriy; Kouznetsova, Valentina L.; Greenberg, Jerry P.; Wrasidlo, Wolf; Overk, Cassia; Gonzalez, Tania; Trejo, Margarita; Spencer, Brian; Kosberg, Kori; Masliah, Eliezer
Molecular Determinants of alpha-Synuclein Mutants' Oligomerization and Membrane Interactions
ACS CHEMICAL NEUROSCIENCE, 6:403-416, MAR 2015
abstract, full text, DOI:10.1021/cn500332w

Tofoleanu, Florentina; Brooks, Bernard R.; Buchete, Nicolae-Viorel
Modulation of Alzheimer's A beta Protofilament-Membrane Interactions by Lipid Headgroups
ACS CHEMICAL NEUROSCIENCE, 6:446-455, MAR 2015
abstract, full text, DOI:10.1021/cn500277f

Pietra, Francesco
From the Sequence to the Conformation of the Unabridged Transmembrane Domains TM1 and TM2 of the cASIC1a Ion Channel - A Parallel Tempering Approach
CHEMISTRY & BIODIVERSITY, 12:350-357, MAR 2015
abstract, full text, DOI:10.1002/cbdv.201400298

Pothapragada, Seetha; Zhang, Peng; Sheriff, Jawaad; Livelli, Mark; Slepian, Marvin J.; Deng, Yuefan; Bluestein, Danny
A phenomenological particle-based platelet model for simulating filopodia formation during early activation
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, 31 Art. No. e02702, MAR 2015
abstract, full text, DOI:10.1002/cnm.2702

Ko, Jeong-Ahn; Kwon, Tae Woo; Ambrosia, Matthew; Ha, Man Yeong
Study of the wetting characteristics of water droplet on a heterogeneous pillared surface
JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY, 29:1243-1256, MAR 2015
abstract, full text, DOI:10.1007/s12206-015-0238-3

Chen, Liao Y.
Erythritol predicted to inhibit permeation of water and solutes through the conducting pore of P. falciparum aquaporin
BIOPHYSICAL CHEMISTRY, 198:14-21, MAR 2015
abstract, full text, DOI:10.1016/j.bpc.2015.01.004

Segrest, Jere P.; Jones, Martin K.; Catte, Andrea; Thirumuruganandham, Saravana P.
A robust all-atom model for LCAT generated by homology modeling
JOURNAL OF LIPID RESEARCH, 56:620-634, MAR 2015
abstract, full text, DOI:10.1194/jlr.M056382

Tovstun, S. A.; Ivanchikhina, A. V.; Nikolenko, L. M.; Nevidimov, A. V.; Brichkin, S. B.; Razumov, V. F.
J-aggregation of a thiacarbocyanine dye in reverse microemulsions
HIGH ENERGY CHEMISTRY, 49:111-116, MAR 2015
abstract, full text, DOI:10.1134/S0018143915020113

Lindert, Steffen; McCammon, J. Andrew
Improved cryoEM-Guided Iterative Molecular Dynamics-Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:1337-1346, MAR 2015
abstract, full text, DOI:10.1021/ct500995d

Miller, John H., Jr.; Villagrau, Martha Y. Suarez; Mark, Sladjana; Briggs, James M.
Normal and impaired charge transport in biological systems
PHYSICA B-CONDENSED MATTER, 460:119-125, MAR 1 2015
abstract, full text, DOI:10.1016/j.physb.2014.11.052

Nicolas, Aurelie; Raguenes-Nicol, Celine; Ben Yaou, Rabah; Ameziane-Le Hir, Sarah; Cheron, Angelique; Vie, Veronique; Claustres, Mireille; Leturcq, France; Delalande, Olivier; Hubert, Jean-Francois; Tuffery-Giraud, Sylvie; Giudice, Emmanuel; Le Rumeur, Elisabeth
Becker muscular dystrophy severity is linked to the structure of dystrophin
HUMAN MOLECULAR GENETICS, 24:1267-1279, MAR 1 2015
abstract, full text, DOI:10.1093/hmg/ddu537

Mondal, Manas; Choudhury, Devapriya; Chakrabarti, Jaydeb; Bhattacharyya, Dhananjay
Role of indirect readout mechanism in TATA box binding protein-DNA interaction
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 29:283-295, MAR 2015
abstract, full text, DOI:10.1007/s10822-014-9828-x

Marek, Ale; Shaffer, Christopher J.; Pepin, Robert; Slovakova, Kristina; Laszlo, Kenneth J.; Bush, Matthew F.; Turecek, Frantiek
Electron Transfer Reduction of the Diazirine Ring in Gas-Phase Peptide Ions. On the Peculiar Loss of [NH4O] from Photoleucine
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 26:415-431, MAR 2015
abstract, full text, DOI:10.1007/s13361-014-1047-0

Cheatham, Thomas E., I.I.I.; Roe, Daniel R.
The Impact of Heterogeneous Computing on Workflows for Biomolecular Simulation and Analysis
COMPUTING IN SCIENCE & ENGINEERING, 17:30-39, MAR-APR 2015
abstract, full text

Liu, Yingzhe; Yu, Tao; Lai, Weipeng; Kang, Ying; Ge, Zhongxue
Ordered and layered structure of liquid nitromethane within a graphene bilayer: toward stabilization of energetic materials through nanoscale confinement
JOURNAL OF MOLECULAR MODELING, 21 Art. No. 40, MAR 2015
abstract, full text, DOI:10.1007/s00894-015-2588-2

Paudyal, Samridhdi; Alfonso-Prieto, Mercedes; Carnevale, Vincenzo; Redhu, Shiv K.; Klein, Michael L.; Nicholson, Allen W.
Combined computational and experimental analysis of a complex of ribonuclease III and the regulatory macrodomain protein, YmdB
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:459-472, MAR 2015
abstract, full text, DOI:10.1002/prot.24751

Baker, Christopher M.
Polarizable force fields for molecular dynamics simulations of biomolecules
WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE, 5:241-254, MAR-APR 2015
abstract, full text, DOI:10.1002/wcms.1215

Zhang, Peng; Zhang, Na; Deng, Yuefan; Bluestein, Danny
A multiple time stepping algorithm for efficient multiscale modeling of platelets flowing in blood plasma
JOURNAL OF COMPUTATIONAL PHYSICS, 284:668-686, MAR 1 2015
abstract, full text, DOI:10.1016/j.jcp.2015.01.004

Ai, Haixin; Zheng, Fangliang; Deng, Fangbo; Zhu, Chunyu; Gu, Ying; Zhang, Li; Li, Xuejiao; Chang, Alan K.; Zhao, Jian; Zhu, Junfeng; Liu, Hongsheng
Structure-Based Virtual Screening for Potential Inhibitors of Influenza A Virus RNA Polymerase PA Subunit
INTERNATIONAL JOURNAL OF PEPTIDE RESEARCH AND THERAPEUTICS, 21:149-156, MAR 2015
abstract, full text, DOI:10.1007/s10989-014-9442-8

Mohan, Rohith R.; Gorham, Ronald D., Jr.; Morikis, Dimitrios
A theoretical view of the C3d:CR2 binding controversy
MOLECULAR IMMUNOLOGY, 64:112-122, MAR 2015
abstract, full text, DOI:10.1016/j.molimm.2014.11.006

Mahboobi, Seyed Hanif; Javanpour, Alex A.; Mofrad, Mohammad R. K.
The Interaction of RNA Helicase DDX3 with HIV-1 Rev-CRM1-RanGTP Complex during the HIV Replication Cycle
PLOS ONE, 10 Art. No. e0112969, FEB 27 2015
abstract, full text, DOI:10.1371/journal.pone.0112969

Shinobu, Ai; Agmon, Noam
The Hole in the Barrel: Water Exchange at the GFP Chromophore
JOURNAL OF PHYSICAL CHEMISTRY B, 119:3464-3478, FEB 26 2015
abstract, full text, DOI:10.1021/jp5127255

Cai, Kaicong; Du, Fenfen; Liu, Jia; Su, Tingting
Solvent induced conformational fluctuation of alanine dipeptide studied by using vibrational probes
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY, 137:701-710, FEB 25 2015
abstract, full text, DOI:10.1016/j.saa.2014.08.126

Johnson, Quentin R.; Lindsay, Richard J.; Nellas, Ricky B.; Fernandez, Elias J.; Shen, Tongye
Mapping Allostery through Computational Glycine Scanning and Correlation Analysis of Residue-Residue Contacts
BIOCHEMISTRY, 54:1534-1541, FEB 24 2015
abstract, full text, DOI:10.1021/bi501152d

Francisca Aguayo, M.; Carlos Caceres, Juan; Fuentealba, Matias; Munoz, Rodrigo; Stange, Claudia; Cabrera, Ricardo; Handford, Michael
Polyol specificity of recombinant Arabidopsis thaliana sorbitol dehydrogenase studied by enzyme kinetics and in silico modeling
FRONTIERS IN PLANT SCIENCE, 6 Art. No. 91, FEB 23 2015
abstract, full text, DOI:10.3389/fpls.2015.00091

Singh, Rajesh; Ahalawat, Navjeet; Murarka, Rajesh K.
Activation of Corticotropin-Releasing Factor 1 Receptor: Insights from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:2806-2817, FEB 19 2015
abstract, full text, DOI:10.1021/jp509814n

Mirjalili, Vahid; Feig, Michael
Interactions of Amino Acid Side-Chain Analogs within Membrane Environments
JOURNAL OF PHYSICAL CHEMISTRY B, 119:2877-2885, FEB 19 2015
abstract, full text, DOI:10.1021/jp511712u

Korchowiec, Beata; Korchowiec, Jacek; Gorczyca, Marcelina; de Vains, Jean-Bernard Regnouf; Rogalska, Ewa
Molecular Organization of Nalidixate Conjugated Calixarenes in Bacterial Model Membranes Probed by Molecular Dynamics Simulation and Langmuir Mono layer Studies
JOURNAL OF PHYSICAL CHEMISTRY B, 119:2990-3000, FEB 19 2015
abstract, full text, DOI:10.1021/jp567151r

Bertran, Oscar; Zhang, Baozhong; Schlueter, A. Dieter; Kroeger, Martin; Aleman, Carlos
Modeling Nanosized Single Molecule Objects: Dendronized Polymers Adsorbed onto Mica
JOURNAL OF PHYSICAL CHEMISTRY C, 119:3746-3753, FEB 19 2015
abstract, full text, DOI:10.1021/jp510586r

Farimani, A. Barati; Heiranian, M.; Aluru, N. R.
Electromechanical Signatures for DNA Sequencing through a Mechanosensitive Nanopore
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:650-657, FEB 19 2015
abstract, full text, DOI:10.1021/jz5025417

Plaschka, C.; Lariviere, L.; Wenzeck, L.; Seizl, M.; Hemann, M.; Tegunov, D.; Petrotchenko, E. V.; Borchers, C. H.; Baumeister, W.; Herzog, F.; Villa, E.; Cramer, P.
Architecture of the RNA polymerase II-Mediator core initiation complex
NATURE, 518:376-380, FEB 19 2015
abstract, full text, DOI:10.1038/nature14229

Huggins, David J.
Quantifying the Entropy of Binding for Water Molecules in Protein Cavities by Computing Correlations
BIOPHYSICAL JOURNAL, 108:928-936, FEB 17 2015
abstract, full text, DOI:10.1016/j.bpj.2014.12.035

Sharma, Vivek; Enkavi, Giray; Vattulainen, Ilpo; Rog, Tomasz; Wikstrom, Marten
Proton-coupled electron transfer and the role of water molecules in proton pumping by cytochrome c oxidase
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:2040-2045, FEB 17 2015
abstract, full text, DOI:10.1073/pnas.1409543112

Wade, Kristin R.; Hotze, Eileen M.; Kuiper, Michael J.; Morton, Craig J.; Parker, Michael W.; Tweten, Rodney K.
An intermolecular electrostatic interaction controls the prepore-to-pore transition in a cholesterol-dependent cytolysin
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:2204-2209, FEB 17 2015
abstract, full text, DOI:10.1073/pnas.1423754112

Cronin, Melissa; Coolbaugh, Michael J.; Nellis, David; Zhu, Jianwei; Wood, David W.; Nussinov, Ruth; Ma, Buyong
Dynamics differentiate between active and inactive inteins
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 91:51-62, FEB 16 2015
abstract, full text, DOI:10.1016/j.ejmech.2014.07.094

Aguayo, Daniel; Pacheco, Nicolas; Morales, Eduardo H.; Collao, Bernardo; Luraschi, Roberto; Cabezas, Carolina; Calderon, Paulina; Gonzalez-Nilo, Fernando; Gil, Fernando; Calderon, Ivan L.; Saavedra, Claudia P.
Hydrogen peroxide and hypochlorous acid influx through the major S. Typhimurium porin OmpD is affected by substitution of key residues of the channel
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 568:38-45, FEB 15 2015
abstract, full text, DOI:10.1016/j.abb.2015.01.005

Hatano, Hiroko; Shaw, Jacqueline; Marquardt, Kaitlin; Zhang, Zhiyong; Gauthier, Laurent; Chanteux, Stephanie; Rossi, Benjamin; Li, Demin; Mitchell, Julie; Kollnberger, Simon
The D0 Ig-like Domain Plays a Central Role in the Stronger Binding of KIR3DL2 to B27 Free H Chain Dimers
JOURNAL OF IMMUNOLOGY, 194:1591-1601, FEB 15 2015
abstract, full text, DOI:10.4049/jimmunol.1402214

Lu, Shouqin; Chen, Shenbao; Mao, Debin; Zhang, Yan; Long, Mian
Contribution of the CR Domain to P-Selectin Lectin Domain Allostery by Regulating the Orientation of the EGF Domain
PLOS ONE, 10 Art. No. e0118083, FEB 12 2015
abstract, full text, DOI:10.1371/journal.pone.0118083

Houari, Ymene; Chibani, Siwar; Jacquemin, Denis; Laurent, Adele D.
TD-DFT Assessment of the Excited State Intramolecular Proton Transfer in Hydroxyphenylbenzimidazole (HBI) Dyes
JOURNAL OF PHYSICAL CHEMISTRY B, 119:2180-2192, FEB 12 2015
abstract, full text, DOI:10.1021/jp505036d

Zhao, Yuqi; Wang, Yanjie; Gao, Yuedong; Li, Gonghua; Huang, Jingfei
Integrated Analysis of Residue Coevolution and Protein Structures Capture Key Protein Sectors in HIV-1 Proteins
PLOS ONE, 10 Art. No. e0117506, FEB 11 2015
abstract, full text, DOI:10.1371/journal.pone.0117506

Banerjee, Shouvik; Wilson, James; Shim, Jiwook; Shankla, Manish; Corbin, Elise A.; Aksimentiev, Aleksei; Bashir, Rashid
Slowing DNA Transport Using Graphene-DNA Interactions
ADVANCED FUNCTIONAL MATERIALS, 25:936-946, FEB 11 2015
abstract, full text, DOI:10.1002/adfm.201403719

Diaz, Natalia; Suarez, Dimas
Extensive Simulations of the Full-Length Matrix Metalloproteinase-2 Enzyme in a Prereactive Complex with a Collagen Triple-Helical Peptide
BIOCHEMISTRY, 54:1243-1258, FEB 10 2015
abstract, full text, DOI:10.1021/bi501014w

Mouchlis, Varnavas D.; Bucher, Denis; McCammon, J. Andrew; Dennis, Edward A.
Membranes serve as allosteric activators of phospholipase A(2), enabling it to extract, bind, and hydrolyze phospholipid substrates
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:E516-E525, FEB 10 2015
abstract, full text, DOI:10.1073/pnas.1424651112

Goldau, Thomas; Murayama, Keiji; Brieke, Clara; Steinwand, Sabrina; Mondal, Padmabati; Biswas, Mithun; Burghardt, Irene; Wachtveitl, Josef; Asanuma, Hiroyuki; Heckel, Alexander
Reversible Photoswitching of RNA Hybridization at Room Temperature with an Azobenzene C-Nucleoside
CHEMISTRY-A EUROPEAN JOURNAL, 21:2845-2854, FEB 9 2015
abstract, full text, DOI:10.1002/chem.201405840

Pal, Somedatta; Chakraborty, Kaushik; Khatua, Prabir; Bandyopadhyay, Sanjoy
Microscopic dynamics of water around unfolded structures of barstar at room temperature
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 055102, FEB 7 2015
abstract, full text, DOI:10.1063/1.4907007

Xu, W.; Lan, Z.; Peng, B. L.; Wen, R. F.; Ma, X. H.
Effect of surface free energies on the heterogeneous nucleation of water droplet: A molecular dynamics simulation approach
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 054701, FEB 7 2015
abstract, full text, DOI:10.1063/1.4906877

Burger, Pieter B.; Williams, Marni; Sprenger, Janina; Reeksting, Shaun B.; Botha, Mariette; Mueller, Ingrid B.; Joubert, Fourie; Birkholtz, Lyn-Marie; Louw, Abraham I.
A novel inhibitor of Plasmodium falciparum spermidine synthase: a twist in the tail
MALARIA JOURNAL, 14 Art. No. 54, FEB 5 2015
abstract, full text, DOI:10.1186/s12936-015-0572-z

Akyuz, Nurunisa; Georgieva, Elka R.; Zhou, Zhou; Stolzenberg, Sebastian; Cuendet, Michel A.; Khelashvili, George; Altman, Roger B.; Terry, Daniel S.; Freed, Jack H.; Weinstein, Harel; Boudker, Olga; Blanchard, Scott C.
Transport domain unlocking sets the uptake rate of an aspartate transporter
NATURE, 518:68-+, FEB 5 2015
abstract, full text, DOI:10.1038/nature14158

Calero, C.; Marti, J.; Guardia, E.
H-1 Nuclear Spin Relaxation of Liquid Water from Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1966-1973, FEB 5 2015
abstract, full text, DOI:10.1021/jp510013q

Luan, Binquan; Tien Huynh; Zhou, Ruhong
Nanopore-Based Sensors for Ligand Receptor Lead Optimization
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:331-337, FEB 5 2015
abstract, full text, DOI:10.1021/jz5025614

Martin, Daniel R.; Matyushov, Dmitry V.
Dipolar Nanodomains in Protein Hydration Shells
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 6:407-412, FEB 5 2015
abstract, full text, DOI:10.1021/jz5025433

De Biase, Pablo M.; Markosyan, Suren; Noskov, Sergei
BROMOC Suite: Monte Carlo/Brownian Dynamics Suite for Studies of Ion Permeation and DNA transport in Biological and Artificial Pores with Effective Potentials
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:264-271, FEB 5 2015
abstract, full text, DOI:10.1002/jcc.23799

Cheung, Luthur Siu-Lun; Shea, Daniel J.; Nicholes, Nathan; Date, Amol; Ostermeier, Marc; Konstantopoulos, Konstantinos
Characterization of Monobody Scaffold Interactions with Ligand via Force Spectroscopy and Steered Molecular Dynamics
SCIENTIFIC REPORTS, 5 Art. No. 8247, FEB 4 2015
abstract, full text, DOI:10.1038/srep08247

Jahangiri, Soran; Legris-Falardeau, Valery; Peslherbe, Gilles H.
Computational investigation of the hydration of alkyl diammonium cations in water clusters
CHEMICAL PHYSICS LETTERS, 621:85-90, FEB 4 2015
abstract, full text, DOI:10.1016/j.cplett.2014.12.045

Eddy, Matthew T.; Andreas, Loren; Teijido, Oscar; Su, Yongchao; Clark, Lindsay; Noskov, Sergei Y.; Wagner, Gerhard; Rostovtseva, Tatiana K.; Griffin, Robert G.
Magic Angle Spinning Nuclear Magnetic Resonance Characterization of Voltage-Dependent Anion Channel Gating in Two-Dimensional Lipid Crystalline Bilayers
BIOCHEMISTRY, 54:994-1005, FEB 3 2015
abstract, full text, DOI:10.1021/bi501260r

Mastrangelo, Eloise; Vachette, Patrice; Cossu, Federica; Malvezzi, Francesca; Bolognesi, Martino; Milani, Mario
The Activator of Apoptosis Smac-DIABLO Acts as a Tetramer in Solution
BIOPHYSICAL JOURNAL, 108:714-723, FEB 3 2015
abstract, full text, DOI:10.1016/j.bpj.2014.11.3471

Hackwon, Do; Kim, Soo Jin; Lee, Chang Woo; Kim, Han-Woo; Park, Hyun Ho; Kim, Ho Min; Park, Hyun; Park, HaJeung; Lee, Jun Hyuck
Crystal structure of UbiX, an aromatic acid decarboxylase from the psychrophilic bacterium Colwellia psychrerythraea that undergoes FMN-induced conformational changes
SCIENTIFIC REPORTS, 5 Art. No. 8196, FEB 3 2015
abstract, full text, DOI:10.1038/srep08196

Bertran, Oscar; del Valle, Luis J.; Revilla-Lopez, Guillermo; Rivas, Manuel; Chaves, Gustavo; Casas, Maria T.; Casanovas, Jordi; Turon, Pau; Puiggali, Jordi; Aleman, Carlos
Synergistic Approach to Elucidate the Incorporation of Magnesium Ions into Hydroxyapatite
CHEMISTRY-A EUROPEAN JOURNAL, 21:2537-2546, FEB 2 2015
abstract, full text, DOI:10.1002/chem.201405428

Park, Yeonju; Seo, Yongil; Chae, Boknam; Pyo, Dongjin; Chung, Hoeil; Hwang, Hyonseok; Jung, Young Mee
Understanding the Structural Differences between Spherical and Rod-Shaped Human Insulin Nanoparticles Produced by Supercritical Fluids Precipitation
CHEMPHYSCHEM, 16:476-482, FEB 2 2015
abstract, full text, DOI:10.1002/cphc.201402504

Chen, Xin; Duan, Danhui; Zhu, Shuyan; Zhang, Jinglai
Investigation of alanine mutations affecting insulin-like growth factor (IGF) I binding to IGF binding proteins
GROWTH FACTORS, 33:40-49, FEB 2015
abstract, full text, DOI:10.3109/08977194.2014.964868

Li Wenzhao; Meng Wei; Tian Pu
Impact of Stable Protein-protein Interaction on Protein Conformational Space
CHEMICAL RESEARCH IN CHINESE UNIVERSITIES, 31:149-155, FEB 2015
abstract, full text, DOI:10.1007/s40242-015-3402-5

Fibriansah, Guntur; Tan, Joanne L.; Smith, Scott A.; de Alwis, Ruklanthi; Ng, Thiam-Seng; Kostyuchenko, Victor A.; Jadi, Ramesh S.; Kukkaro, Petra; de Silva, Aravinda M.; Crowe, James E.; Lok, Shee-Mei
A highly potent human antibody neutralizes dengue virus serotype 3 by binding across three surface proteins
NATURE COMMUNICATIONS, 6 Art. No. 6341, FEB 2015
abstract, full text, DOI:10.1038/ncomms7341

Barakat, Khaled H.; Anwar-Mohamed, Anwar; Tuszynski, Jack A.; Robins, Morris J.; Tyrrell, D. Lorne; Houghton, Michael
A Refined Model of the HCV NS5A Protein Bound to Daclatasvir Explains Drug-Resistant Mutations and Activity against Divergent Genotypes
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 55:362-373, FEB 2015
abstract, full text, DOI:10.1021/ci400631n

Sandberg, Robert B.; Banchelli, Martina; Guardiani, Carlo; Menichetti, Stefano; Caminati, Gabriella; Procacci, Piero
Efficient Nonequilibrium Method for Binding Free Energy Calculations in Molecular Dynamics Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:423-435, FEB 2015
abstract, full text, DOI:10.1021/ct500964e

Hardy, David J.; Wu, Zhe; Phillips, James C.; Stone, John E.; Skeel, Robert D.; Schulten, Klaus
Multilevel Summation Method for Electrostatic Force Evaluation
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:766-779, FEB 2015
abstract, full text, TCBG publications, DOI:10.1021/ct5009075

Zwier, Matthew C.; Adelman, Joshua L.; Kaus, Joseph W.; Pratt, Adam J.; Wong, Kim F.; Rego, Nicholas B.; Suarez, Ernesto; Lettieri, Steven; Wang, David W.; Grabe, Michael; Zuckerman, Daniel M.; Chong, Lillian T.
WESTPA: An Interoperable, Highly Scalable Software Package for Weighted Ensemble Simulation and Analysis
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:800-809, FEB 2015
abstract, full text, DOI:10.1021/ct5010615

Sieradzan, Adam K.; Krupa, Pawel; Scheraga, Harold A.; Liwo, Adam; Czaplewski, Cezary
Physics-Based Potentials for the Coupling between Backbone- and Side-Chain-Local Conformational States in the United Residue (UNRES) Force Field for Protein Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:817-831, FEB 2015
abstract, full text, DOI:10.1021/ct500736a

Modi, Niraj; Barcena-Uribarri, Ivan; Bains, Manjeet; Benz, Roland; Hancock, Robert E. W.; Kleinekathoefer, Ulrich
Tuning the Affinity of Anion Binding Sites in Porin Channels with Negatively Charged Residues: Molecular Details for OprP
ACS CHEMICAL BIOLOGY, 10:441-451, FEB 2015
abstract, full text, DOI:10.1021/cb500399j

Desdouits, Nathan; Nilges, Michael; Blondel, Arnaud
Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 55:13-24, FEB 2015
abstract, full text, DOI:10.1016/j.jmgm.2014.10.011

Li, Chen-Yu; Hemmig, Elise A.; Kong, Jinglin; Yoo, Jejoong; Hernandez-Ainsa, Silvia; Keyser, Ulrich F.; Aksimentiev, Aleksei
Ionic Conductivity, Structural Deformation, and Programmable Anisotropy of DNA Origami in Electric Field
ACS NANO, 9:1420-1433, FEB 2015
abstract, full text, DOI:10.1021/nn505825z

Li Jun-Wei; Xiao Shao-Ying; Xie Xiao-Xiao; Yu Hui; Zhang Hai-Lin; Zhan Yong; An Hai-Long
Identification of Three Interactions to Determine the Conformation Change and to Maintain the Function of Kir2.1 Channel Protein
CHINESE PHYSICS LETTERS, 32 Art. No. 028702, FEB 2015
abstract, full text, DOI:10.1088/0256-307X/32/2/028702

Madsen, J. J.; Persson, E.; Olsen, O. H.
Tissue factor activates allosteric networks in factor VIIa through structural and dynamic changes
JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 13:262-267, FEB 2015
abstract, full text, DOI:10.1111/jth.12791

Yu, Xiaofeng; Cojocaru, Vlad; Mustafa, Ghulam; Salo-Ahen, Outi M. H.; Lepesheva, Galina I.; Wade, Rebecca C.
Dynamics of CYP51: implications for function and inhibitor design
JOURNAL OF MOLECULAR RECOGNITION, 28:59-73, FEB 2015
abstract, full text, DOI:10.1002/jmr.2412

Noto, Rosina; Santangelo, Maria Grazia; Levantino, Matteo; Cupane, Antonio; Mangione, Maria Rosalia; Parisi, Daniele; Ricagno, Stefano; Bolognesi, Martino; Manno, Mauro; Martorana, Vincenzo
Functional and dysfunctional conformers of human neuroserpin characterized by optical spectroscopies and Molecular Dynamics
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1854:110-117, FEB 2015
abstract, full text, DOI:10.1016/j.bbapap.2014.10.002

Moreau, Adrien; Gosselin-Badaroudine, Pascal; Delemotte, Lucie; Klein, Michael L.; Chahine, Mohamed
Gating pore currents are defects in common with two Na(v)1.5 mutations in patients with mixed arrhythmias and dilated cardiomyopathy
JOURNAL OF GENERAL PHYSIOLOGY, 145:93-106, FEB 2015
abstract, full text, DOI:10.1085/jgp.201411304

Davis, Adam S.; Federici, Thais; Ray, William C.; Boulis, Nicholas M.; O'Connor, Deirdre; Clark, K. Reed; Bartlett, Jeffrey S.
Rational Design and Engineering of a Modified Adeno-Associated Virus (AAV1)-Based Vector System for Enhanced Retrograde Gene Delivery
NEUROSURGERY, 76:216-225, FEB 2015
abstract, full text, DOI:10.1227/NEU.0000000000000589

Zhang, Rui; Bhattacharjee, Anirban; Field, Martin J.; Salahub, Dennis R.
Multiple proton relay routes in the reaction mechanism of RNAP II: Assessing the effect of structural model
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:268-281, FEB 2015
abstract, full text, DOI:10.1002/prot.24732

Langley, David R.; Kimura, S. Roy; Sivaprakasam, Prasanna; Zhou, Nannan; Dicker, Ira; McAuliffe, Brian; Wang, Tao; Kadow, John F.; Meanwell, Nicholas A.; Krystal, Mark
Homology models of the HIV-1 attachment inhibitor BMS-626529 bound to gp120 suggest a unique mechanism of action
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:331-350, FEB 2015
abstract, full text, DOI:10.1002/prot.24726

Kolsek, Katra; Gobec, Martina; Rascan, Irena Minaric; Dolenc, Marija Sollner
Screening of bisphenol A, triclosan and paraben analogues as modulators of the glucocorticoid and androgen receptor activities
TOXICOLOGY IN VITRO, 29:8-15, FEB 2015
abstract, full text, DOI:10.1016/j.tiv.2014.08.009

Zhang, Chongqian; Du, Chunmiao; Feng, Zhiwei; Zhu, Jingyu; Li, Youyong
Hologram Quantitative Structure Activity Relationship, Docking, and Molecular Dynamics Studies of Inhibitors for CXCR4
CHEMICAL BIOLOGY & DRUG DESIGN, 85:119-136, FEB 2015
abstract, full text, DOI:10.1111/cbdd.12377

Hamed, Elham; Ma, Dan; Keten, Sinan
Multiple PEG Chains Attached onto the Surface of a Helix Bundle: Conformations and Implications
ACS BIOMATERIALS-SCIENCE & ENGINEERING, 1:79-84, FEB 2015
abstract, full text, DOI:10.1021/ab500088b

Wang, Beibei; Opron, Kristopher; Burton, Zachary F.; Cukier, Robert I.; Feig, Michael
Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details
NUCLEIC ACIDS RESEARCH, 43:1133-1146, JAN 30 2015
abstract, full text, DOI:10.1093/nar/gku1370

Sormanni, Pietro; Aprile, Francesco A.; Vendruscolo, Michele
The CamSol Method of Rational Design of Protein Mutants with Enhanced Solubility
JOURNAL OF MOLECULAR BIOLOGY, 427:478-490, JAN 30 2015
abstract, full text, DOI:10.1016/j.jmb.2014.09.026

Zheng, Fan; Jewell, Heather; Fitzpatrick, Jeremy; Zhang, Jian; Mierke, Dale F.; Grigoryan, Gevorg
Computational Design of Selective Peptides to Discriminate between Similar PDZ Domains in an Oncogenic Pathway
JOURNAL OF MOLECULAR BIOLOGY, 427:491-510, JAN 30 2015
abstract, full text, DOI:10.1016/j.jmb.2014.10.014

Darre, Leonardo; Furini, Simone; Domene, Carmen
Permeation and Dynamics of an Open-Activated TRPV1 Channel
JOURNAL OF MOLECULAR BIOLOGY, 427:537-549, JAN 30 2015
abstract, full text, DOI:10.1016/j.jmb.2014.11.016

Freudenthal, Bret D.; Beard, William A.; Perera, Lalith; Shock, David D.; Kim, Taejin; Schlick, Tamar; Wilson, Samuel H.
Uncovering the polymerase-induced cytotoxicity of an oxidized nucleotide
NATURE, 517:635-U261, JAN 29 2015
abstract, full text, DOI:10.1038/nature13886

Li, Jun; Deng, Mingsen; Voronine, Dmitri V.; Mukamel, Shaul; Jiang, Jun
Two-Dimensional Near Ultraviolet (2DNUV) Spectroscopic Probe of Structural-Dependent Exciton Dynamics in a Protein
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1314-1322, JAN 29 2015
abstract, full text, DOI:10.1021/jp509314y

Meng, Yilin; Lin, Yen-lin; Roux, Benoit
Computational Study of the "DFG-Flip" Conformational Transition in c-Abl and c-Src Tyrosine Kinases
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1443-1456, JAN 29 2015
abstract, full text, DOI:10.1021/jp511792a

Samoylova, Olga N.; Calixte, Emvia I.; Shuford, Kevin L.
Molecular Dynamics Simulations of Ion Transport in Carbon Nanotube Channels
JOURNAL OF PHYSICAL CHEMISTRY C, 119:1659-1666, JAN 29 2015
abstract, full text, DOI:10.1021/jp5103669

Luedemann, Gesa; Solov'yov, Ilia A.; Kubar, Tomas; Elstner, Marcus
Solvent Driving Force Ensures Fast Formation of a Persistent and Well-Separated Radical Pair in Plant Cryptochrome
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 137:1147-1156, JAN 28 2015
abstract, full text, DOI:10.1021/ja510550g

Chakraborty, Srirupa; Zheng, Wenjun
Decrypting the Structural, Dynamic, and Energetic Basis of a Monomeric Kinesin Interacting with a Tubulin Dimer in Three ATPase States by All-Atom Molecular Dynamics Simulation
BIOCHEMISTRY, 54:859-869, JAN 27 2015
abstract, full text, DOI:10.1021/bi501056h

Francois-Heude, Marc; Mendez-Ardoy, Alejandro; Cendret, Virginie; Lafite, Pierre; Daniellou, Richard; Ortiz Mellet, Carmen; Garcia Fernandez, Jose M.; Moreau, Vincent; Djedaini-Pilard, Florence
Synthesis of High-Mannose Oligosaccharide Analogues through Click Chemistry: True Functional Mimics of Their Natural Counterparts Against Lectins?
CHEMISTRY-A EUROPEAN JOURNAL, 21:1978-1991, JAN 26 2015
abstract, full text, DOI:10.1002/chem.201405481

Poblete, Horacio; Oyarzun, Ingrid; Olivero, Pablo; Comer, Jeffrey; Zuniga, Matias; Sepulveda, Ronnina V.; Baez-Nieto, David; Gonzalez Leon, Carlos; Gonzalez-Nilo, Fernando; Latorre, Ramon
Molecular Determinants of Phosphatidylinositol 4,5-Bisphosphate (PI(4,5)P-2) Binding to Transient Receptor Potential V1 (TRPV1) Channels
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:2086-2098, JAN 23 2015
abstract, full text, DOI:10.1074/jbc.M114.613620

Patel, Dhilon S.; He, Xibing; MacKerell, Alexander D., Jr.
Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator
JOURNAL OF PHYSICAL CHEMISTRY B, 119:637-652, JAN 22 2015
abstract, full text, DOI:10.1021/jp412696m

Krzeminska, Agnieszka; Paneth, Piotr; Moliner, Vicent; Swiderek, Katarzyna
Binding Isotope Effects as a Tool for Distinguishing Hydrophobic and Hydrophilic Binding Sites of HIV-1 RT
JOURNAL OF PHYSICAL CHEMISTRY B, 119:917-927, JAN 22 2015
abstract, full text, DOI:10.1021/jp506119h

Ellingson, Sally R.; Miao, Yinglong; Baudry, Jerome; Smith, Jeremy C.
Multi-Conformer Ensemble Docking to Difficult Protein Targets
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1026-1034, JAN 22 2015
abstract, full text, DOI:10.1021/jp506511p

Craft, John W., Jr.; Shen, Tsai-wei; Brier, Lindsey M.; Briggs, James M.
Biophysical Characteristics of Cholera Toxin and Escherichia coli Heat-Labile Enterotoxin Structure and Chemistry Lead to Differential Toxicity
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1048-1061, JAN 22 2015
abstract, full text, DOI:10.1021/jp506509c

Comer, Jeffrey; Gumbart, James C.; Henin, Jerome; Lelievre, Tony; Pohorille, Andrew; Chipot, Christophe
The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1129-1151, JAN 22 2015
abstract, full text, DOI:10.1021/jp506633n

Gianti, Eleonora; Carnevale, Vincenzo; DeGrado, William F.; Klein, Michael L.; Fiorin, Giacomo
Hydrogen-Bonded Water Molecules in the M2 Channel of the Influenza A Virus Guide the Binding Preferences of Ammonium-Based Inhibitors
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1173-1183, JAN 22 2015
abstract, full text, DOI:10.1021/jp506807y

Gleed, Mitchell L.; Busath, David D.
Why Bound Amantadine Fails to Inhibit Proton Conductance According to Simulations of the Drug-Resistant Influenza A M2 (S31N)
JOURNAL OF PHYSICAL CHEMISTRY B, 119:1225-1231, JAN 22 2015
abstract, full text, DOI:10.1021/jp508545d

Holden, Jeffrey K.; Kang, Soosung; Hollingsworth, Scott A.; Li, Huiying; Lim, Nathan; Chen, Steven; Huang, He; Xue, Fengtian; Tang, Wei; Silverman, Richard B.; Poulos, Thomas L.
Structure-Based Design of Bacterial Nitric Oxide Synthase Inhibitors
JOURNAL OF MEDICINAL CHEMISTRY, 58:994-1004, JAN 22 2015
abstract, full text, DOI:10.1021/jm501723p

Schur, Florian K. M.; Hagen, Wim J. H.; Rumlova, Michaela; Ruml, Tomas; Mueller, Barbara; Kraeusslich, Hans-Georg; Briggs, John A. G.
Structure of the immature HIV-1 capsid in intact virus particles at 8.8 angstrom resolution
NATURE, 517:505-508, JAN 22 2015
abstract, full text, DOI:10.1038/nature13838

Gun'ko, Vladimir M.; Nasiri, Rasoul; Sazhin, Sergei S.
Effects of the surroundings and conformerisation of n-dodecane molecules on evaporation/condensation processes
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 034502, JAN 21 2015
abstract, full text, DOI:10.1063/1A905496

Harrach, Michael F.; Klameth, Felix; Drossel, Barbara; Vogel, Michael
Effect of the hydroaffinity and topology of pore walls on the structure and dynamics of confined water
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 034703, JAN 21 2015
abstract, full text, DOI:10.1063/1.4905557

Lindert, Steffen; Cheng, Yuanhua; Kekenes-Huskey, Peter; Regnier, Michael; McCammon, J. Andrew
Effects of HCM cTnI Mutation R145G on Troponin Structure and Modulation by PKA Phosphorylation Elucidated by Molecular Dynamics Simulations
BIOPHYSICAL JOURNAL, 108:395-407, JAN 20 2015
abstract, full text, DOI:10.1016/j.bpj.2014.11.3461

Chamberlin, Adam; Qiu, Feng; Wang, Yibo; Noskov, Sergei Y.; Larsson, H. Peter
Mapping the Gating and Permeation Pathways in the Voltage-Gated Proton Channel Hv1
JOURNAL OF MOLECULAR BIOLOGY, 427:131-145, JAN 16 2015
abstract, full text, DOI:10.1016/j.jmb.2014.11.018

Yan, Si; Zhang, Huilan; Hou, Guangjin; Ahmed, Shubbir; Williams, John C.; Polenova, Tatyana
Internal Dynamics of Dynactin CAP-Gly Is Regulated by Microtubules and Plus End Tracking Protein EB1
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:1607-1622, JAN 16 2015
abstract, full text, DOI:10.1074/jbc.M114.603118

Barragan, Angela M.; Crofts, Antony R.; Schulten, Klaus; Solov'yov, Ilia A.
Identification of Ubiquinol Binding Motifs at the Q(o)-Site of the Cytochrome bc(1) Complex
JOURNAL OF PHYSICAL CHEMISTRY B, 119:433-447, JAN 15 2015
abstract, full text, TCBG publications, DOI:10.1021/jp510022w

Miller, Yifat; Ma, Buyong; Nussinov, Ruth
Polymorphism in Self-Assembly of Peptide-Based beta-Hairpin Contributes to Network Morphology and Hydrogel Mechanical Rigidity
JOURNAL OF PHYSICAL CHEMISTRY B, 119:482-490, JAN 15 2015
abstract, full text, DOI:10.1021/jp511485n

Mejri, Alia; Vardanega, Delphine; Tangour, Bahoueddine; Gharbi, Tijani; Picaud, Fabien
Encapsulation into Carbon Nanotubes and Release of Anticancer Cisplatin Drug Molecule
JOURNAL OF PHYSICAL CHEMISTRY B, 119:604-611, JAN 15 2015
abstract, full text, DOI:10.1021/jp5102384

Li, Chunyu; Strachan, Alejandro
Molecular Scale Simulations on Thermoset Polymers: A Review
JOURNAL OF POLYMER SCIENCE PART B-POLYMER PHYSICS, 53:103-122, JAN 15 2015
abstract, full text, DOI:10.1002/polb.23489

Tao, Jinhui; Battle, Keith C.; Pan, Haihua; Salter, E. Alan; Chien, Yung-Ching; Wierzbicki, Andrzej; De Yoreo, James J.
Energetic basis for the molecular-scale organization of bone
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 112:326-331, JAN 13 2015
abstract, full text, DOI:10.1073/pnas.1404481112

He Jia; Feng Xizeng; Shao Xueguang; Cai Wensheng
Adsorption Behavior of Hydrophobin Proteins on Surface of Mica
CHEMICAL JOURNAL OF CHINESE UNIVERSITIES-CHINESE, 36:110-115, JAN 10 2015
abstract, full text, DOI:10.7503/cjcu20140808

Baul, Upayan; Vemparala, Satyavani
Ion hydration and associated defects in hydrogen bond network of water: Observation of reorientationally slow water molecules beyond first hydration shell in aqueous solutions of MgCl2
PHYSICAL REVIEW E, 91 Art. No. 012114, JAN 8 2015
abstract, full text, DOI:10.1103/PhysRevE.91.012114

Cui, Di; Ou, Shu-Ching; Patel, Sandeep
Protein Denaturants at Aqueous-Hydrophobic Interfaces: Self-Consistent Correlation between Induced Interfacial Fluctuations and Denaturant Stability at the Interface
JOURNAL OF PHYSICAL CHEMISTRY B, 119:164-178, JAN 8 2015
abstract, full text, DOI:10.1021/jp507203g

Polak, Andraz; Velikonja, Aljaz; Kramar, Peter; Tarek, Mounir; Miklavcic, Damijan
Electroporation Threshold of POPC Lipid Bilayers with Incorporated Polyoxyethylene Glycol (C12E8)
JOURNAL OF PHYSICAL CHEMISTRY B, 119:192-200, JAN 8 2015
abstract, full text, DOI:10.1021/jp509789m

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy
Effect of temperature on the low-frequency vibrational spectrum and relative structuring of hydration water around a single-stranded DNA
JOURNAL OF CHEMICAL PHYSICS, 142 Art. No. 015101, JAN 7 2015
abstract, full text, DOI:10.1063/1.4904896

Kim, Hanseong; Zou, Taisong; Modi, Chintan; Doerner, Katerina; Grunkemeyer, Timothy J.; Chen, Liqing; Fromme, Raimund; Matz, Mikhail V.; Ozkan, S. Banu; Wachter, Rebekka M.
A Hinge Migration Mechanism Unlocks the Evolution of Green-to-Red Photoconversion in GFP-like Proteins
STRUCTURE, 23:34-43, JAN 6 2015
abstract, full text, DOI:10.1016/j.str.2014.11.011

Baker, Joseph L.; Courtemanche, Naomi; Parton, Daniel L.; McCullagh, Martin; Pollard, Thomas D.; Voth, Gregory A.
Electrostatic Interactions between the Bni1p Formin FH2 Domain and Actin Influence Actin Filament Nucleation
STRUCTURE, 23:68-79, JAN 6 2015
abstract, full text, DOI:10.1016/j.str.2014.10.014

Dai, Jian; Zhou, Huan-Xiang
Reduced Curvature of Ligand-Binding Domain Free-Energy Surface Underlies Partial Agonism at NMDA Receptors
STRUCTURE, 23:228-236, JAN 6 2015
abstract, full text, DOI:10.1016/j.str.2014.11.012

Huang, Wei; Ravikumar, Krishnakumar M.; Chance, Mark R.; Yang, Sichun
Quantitative Mapping of Protein Structure by Hydroxyl Radical Footprinting-Mediated Structural Mass Spectrometry: A Protection Factor Analysis
BIOPHYSICAL JOURNAL, 108:107-115, JAN 6 2015
abstract, full text, DOI:10.1016/j.bpj.2014.11.013

Kasimova, Marina A.; Zaydman, Mark A.; Cui, Jianmin; Tarek, Mounir
PIP2-dependent coupling is prominent in Kv7.1 due to weakened interactions between S4-S5 and S6
SCIENTIFIC REPORTS, 5 Art. No. 7474, JAN 6 2015
abstract, full text, DOI:10.1038/srep07474

Xu, Ji; Li, Xiaoxia; Hou, Chaofeng; Wang, Limin; Zhou, Guangzheng; Ge, Wei; Li, Jinghai
Engineering molecular dynamics simulation in chemical engineering
CHEMICAL ENGINEERING SCIENCE, 121:200-216, JAN 6 2015
abstract, full text, DOI:10.1016/j.ces.2014.09.051

Rovigatti, Lorenzo; Sulc, Petr; Reguly, Istvan Z.; Romano, Flavio
A Comparison between Parallelization Approaches in Molecular Dynamics Simulations on GPUs
JOURNAL OF COMPUTATIONAL CHEMISTRY, 36:1-8, JAN 5 2015
abstract, full text, DOI:10.1002/jcc.23763

Zomot, Elia; Gur, Mert; Bahar, Ivet
Microseconds Simulations Reveal a New Sodium-binding Site and the Mechanism of Sodium-coupled Substrate Uptake by LeuT
JOURNAL OF BIOLOGICAL CHEMISTRY, 290:544-555, JAN 2 2015
abstract, full text, DOI:10.1074/jbc.M114.617555

Bujalowski, Paul J.; Nicholls, Paul; Barral, Jose M.; Oberhauser, Andres F.
Thermally-induced structural changes in an armadillo repeat protein suggest a novel thermosensor mechanism in a molecular chaperone
FEBS LETTERS, 589:123-130, JAN 2 2015
abstract, full text, DOI:10.1016/j.febslet.2014.11.034

Sellers, Michael S.; Lisal, Martin; Brennan, John K.
Exponential-six potential scaling for the calculation of free energies in molecular simulations
MOLECULAR PHYSICS, 113:45-54, JAN 2 2015
abstract, full text, DOI:10.1080/00268976.2014.942405

Ma, Cheng-Wei; Xiu, Zhi-Long; Zeng, An-Ping
Exploring signal transduction in heteromultimeric protein based on energy dissipation model
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:134-146, JAN 2 2015
abstract, full text, DOI:10.1080/07391102.2013.855145

Fu, Yi; Chen, Zhiguo; Zhao, Ji
MOLECULAR DYNAMICS SIMULATION TO ELUCIDATE THE THERMOSTABILITY OF B DOMAIN IN CGTASE
THEORETICAL BIOLOGY FORUM, 108:57-73, 2015
abstract, full text

Sotomayor, Marcos
Computational Exploration of Single-Protein Mechanics by Steered Molecular Dynamics
MECHANICS OF HEARING: PROTEIN TO PERCEPTION, 1703 Art. No. 030001, 2015
abstract, full text, DOI:10.1063/1.4939316

Koussa, Mounir A.; Sotomayor, Marcos; Wong, Wesley P.; Corey, David P.
Towards Force Spectroscopy of Single Tip-Link Bonds
MECHANICS OF HEARING: PROTEIN TO PERCEPTION, 1703 Art. No. 030002, 2015
abstract, full text, DOI:10.1063/1.4939317

Bussi, Giovanni; Branduardi, Davide
Free-Energy Calculations with Metadynamics: Theory and Practice
REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 28, 28:1-49, 2015
full text

Shi, Yue; Ren, Pengyu; Schnieders, Michael; Piquemal, Jean-Philip
Polarizable Force Fields for Biomolecular Modeling
REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 28, 28:51-86, 2015
full text

Towse, Clare-Louise; Daggett, Valerie
Modeling Protein Folding Pathways
REVIEWS IN COMPUTATIONAL CHEMISTRY, VOL 28, 28:87-135, 2015
full text

Blackburn, Elizabeth A.; Wear, Martin A.; Landre, Vivian; Narayan, Vikram; Ning, Jia; Erman, Burak; Ball, Kathryn L.; Walkinshaw, Malcolm D.
Cyclophilin40 isomerase activity is regulated by a temperature-dependent allosteric interaction with Hsp90
BIOSCIENCE REPORTS, 35 Art. No. e00258, 2015
abstract, full text, DOI:10.1042/BSR20150124

Zmejev, D.N.; Klimov, A.V.; Levchenko, N.N.; Okunev, A.S.; Stempkovsky, A.L.
Emulation on Hardware and Software of the Parallel Computing Streaming System "Buran"
Informatsionnye tekhnologii, 21:757-763, 2015
abstract, full text

Abdizadeh, Haleh; Guven, Gokce; Atilgan, Ali Rana; Atilgan, Canan
Perturbation response scanning specifies key regions in subtilisin serine protease for both function and stability
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 30:867-873, 2015
abstract, full text, DOI:10.3109/14756366.2014.979345

Hernandez, Monica L.; Dreher, Matthieu; Barrios, Carlos J.; Raffin, Bruno
Asynchronous in Situ Processing with Gromacs: Taking Advantage of GPUs
HIGH PERFORMANCE COMPUTING, CARLA 2015, 565:89-106, 2015
abstract, full text, DOI:10.1007/978-3-319-26928-3_7

Culka, Martin; Milichovsky, Jan; Jerabek, Petr; Stiborova, Marie; Martinek, Vaclav
Ferrous and ferric state of cytochromes P450 in intact Escherichia coli cells: a possible role of cytochrome P450-flavodoxin interactions
NEUROENDOCRINOLOGY LETTERS, 36:29-37, 2015
abstract, full text

Badu, Shyam; Melnik, Roderick; Prabhakar, Sanjay
RNA Nanostructures in Physiological Solutions: Multiscale Modeling and Applications
PHYSICS OF LIQUID MATTER: MODERN PROBLEMS, 171:337-355, 2015
abstract, full text, DOI:10.1007/978-3-319-20875-6_13

Mak, Michael; Kim, Taeyoon; Zaman, Muhammad H.; Kamm, Roger D.
Multiscale mechanobiology: computational models for integrating molecules to multicellular systems
INTEGRATIVE BIOLOGY, 7:1093-1108, 2015
abstract, full text, DOI:10.1039/c5ib00043b

Truong, Tiffany; Shams, Hengameh; Mofrad, Mohammad R. K.
Mechanisms of integrin and filamin binding and their interplay with talin during early focal adhesion formation
INTEGRATIVE BIOLOGY, 7:1285-1296, 2015
abstract, full text, DOI:10.1039/c5ib00133a

Grigoriev, F. V.; Sulimov, A. V.; Kochikov, I. V.; Kondakova, O. A.; Sulimov, V. B.; Tikhonravov, A. V.
Supercomputer modeling of the ion beam sputtering process: full-atomistic level
OPTICAL SYSTEMS DESIGN 2015: ADVANCES IN OPTICAL THIN FILMS V, 9627 Art. No. 962708, 2015
abstract, full text, DOI:10.1117/12.2190938

Simonovsky, Eyal; Kozlowski, Henryk; Miller, Yifat
Termini capping of metal-poly-His peptide complexes induces the formation of alpha-helix
RSC ADVANCES, 5:104551-104555, 2015
abstract, full text, DOI:10.1039/c5ra15385a

Liubysh, O. O.; Vlasiuk, A. V.; Perepelytsya, S. M.
STRUCTURIZATION OF COUNTERIONS AROUND DNA DOUBLE HELIX: A MOLECULAR DYNAMICS STUDY
UKRAINIAN JOURNAL OF PHYSICS, 60:433-442, 2015
abstract, full text

Mannoor, Madhusoodanan; Kang, Sangmo; Suh, Yong Kweon
Molecular Dynamics Simulation of Aggregates in the Dodecane/span80 System and Their Behaviour in an Electric Field
ADVANCES IN CONDENSED MATTER PHYSICS, Art. No. 739458, 2015
abstract, full text, DOI:10.1155/2015/739458

Velichko, Elena; Zezina, Tatyana; Cheremiskina, Anastasia; Tsybin, Oleg
Nano Communication Device with Embedded Molecular Films: Effect of Electromagnetic Field and Dipole Moment Dynamics
INTERNET OF THINGS, SMART SPACES, AND NEXT GENERATION NETWORKS AND SYSTEMS, 9247:765-771, 2015
abstract, full text, DOI:10.1007/978-3-319-23126-6_71

Mertz, Blake; Feng, Jun; Corcoran, Conor; Neeley, Brandon
Explaining the mobility of retinal in activated rhodopsin and opsin
PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES, 14:1952-1964, 2015
abstract, full text, DOI:10.1039/c5pp00173k

Gao, Lu; Liu, Wenhao; Lee, One-Sun; Dmochowski, Ivan J.; Saven, Jeffery G.
Xe affinities of water-soluble cryptophanes and the role of confined water
CHEMICAL SCIENCE, 6:7238-7248, 2015
abstract, full text, DOI:10.1039/c5sc02401c

Nandy, Bidisha; Saurabh, Suman; Sahoo, Anil Kumar; Dixit, Narendra M.; Maiti, Prabal K.
The SPL7013 dendrimer destabilizes the HIV-1 gp120-CD4 complex
NANOSCALE, 7:18628-18641, 2015
abstract, full text, DOI:10.1039/c5nr04632g

Spata, Vincent A.; Matsika, Spiridoula
Photophysical deactivation pathways in adenine oligonucleotides
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:31073-31083, 2015
abstract, full text, DOI:10.1039/c5cp04254b

Cordeiro, Jhonatam; Desai, Salil
lPROCESS PARAMETER STUDIES OF MOLECULAR DYNAMICS MODELS TO CONTROL SUBSTRATE WETTABILITY
PROCEEDINGS OF THE ASME 10TH INTERNATIONAL MANUFACTURING SCIENCE AND ENGINEERING CONFERENCE, 2015, VOL 1, Art. No. V001T02A025, 2015
abstract, full text

Fu, Haohao; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
Why do the structural properties of complexes formed by glucans and carbon nanotubes differ so much?
RSC ADVANCES, 5:95682-95689, 2015
abstract, full text, DOI:10.1039/c5ra17472d

Majhi, Amit Kumar; Kanchi, Subbarao; Venkataraman, V.; Ayappa, K. G.; Maiti, Prabal K.
Estimation of activation energy for electroporation and pore growth rate in liquid crystalline and gel phases of lipid bilayers using molecular dynamics simulations
SOFT MATTER, 11:8632-8640, 2015
abstract, full text, DOI:10.1039/c5sm02029h

Cozza, Giorgio; Venerando, Andrea; Sarno, Stefania; Pinna, Lorenzo A.
The Selectivity of CK2 Inhibitor Quinalizarin: A Reevaluation
BIOMED RESEARCH INTERNATIONAL, Art. No. 734127, 2015
abstract, full text, DOI:10.1155/2015/734127

Teo, Ruijie D.; Dong, Sijia S.; Gross, Zeev; Gray, Harry B.; Goddard, William A., I.I.I.
Computational predictions of corroles as a class of Hsp90 inhibitors
MOLECULAR BIOSYSTEMS, 11:2907-2914, 2015
abstract, full text, DOI:10.1039/c5mb00352k

Duan, Mei Lin; Liu, Lin; Du, Juan; Yao, Xiao Jun
pH effects on the structural dynamics of cutinase from Trichoderma reesei: insights from molecular dynamics simulations
MOLECULAR BIOSYSTEMS, 11:3149-3155, 2015
abstract, full text, DOI:10.1039/c5mb00467e

Galano-Frutos, Juan J.; Carmen Moron, M.; Sancho, Javier
The mechanism of water/ion exchange at a protein surface: a weakly bound chloride in Helicobacter pylori apoflavodoxin
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:28635-28646, 2015
abstract, full text, DOI:10.1039/c5cp04504e

Yagi, Kiyoshi; Li, Pai-Chi; Shirota, Koichiro; Kobayashi, Toshihide; Sugita, Yuji
A weight averaged approach for predicting amide vibrational bands of a sphingomyelin bilayer
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:29113-29123, 2015
abstract, full text, DOI:10.1039/c5cp04131g

Gong, Huichao; Zhang, Sai; Wang, Jiangdian; Gong, Haipeng; Zeng, Jianyang
Constructing Structure Ensembles of Intrinsically Disordered Proteins from Chemical Shift Data
RESEARCH IN COMPUTATIONAL MOLECULAR BIOLOGY (RECOMB 2015), 9029:108-121, 2015
abstract, full text, DOI:10.1007/978-3-319-16706-0_13

Merzhievskii, L.A.
Deformation Models under Intense Dynamic Loading (Review)
Fizika goreniya i vzryva, 51:144-160, 2015
abstract, full text

Forsythe, Jay G.; Petrov, Anton S.; Walker, Chelsea A.; Allen, Samuel J.; Pellissier, Jarrod S.; Bush, Matthew F.; Hud, Nicholas V.; Fernandez, Facundo M.
Collision cross section calibrants for negative ion mode traveling wave ion mobility-mass spectrometry
ANALYST, 14:6853-6861, 2015
abstract, full text, DOI:10.1039/c5an00946d

Palermo, Mattia Felice; Muccioli, Luca; Zannoni, Claudio
Molecular organization in freely suspended nano-thick 8CB smectic films. An atomistic simulation
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:26149-26159, 2015
abstract, full text, DOI:10.1039/c5cp04213e

Autzen, Henriette Elisabeth; Siuda, Iwona; Sonntag, Yonathan; Nissen, Poul; Moller, Jesper Vuust; Thogersen, Lea
Regulation of the Ca2+-ATPase by cholesterol: A specific or non-specific effect?
MOLECULAR MEMBRANE BIOLOGY, 32:75-87, 2015
abstract, full text, DOI:10.3109/09687688.2015.1073382

Duan, Guangxin; Kang, Seung-gu; Tian, Xin; Garate, Jose Antonio; Zhao, Lin; Ge, Cuicui; Zhou, Ruhong
Protein corona mitigates the cytotoxicity of graphene oxide by reducing its physical interaction with cell membrane
NANOSCALE, 7:15214-15224, 2015
abstract, full text, DOI:10.1039/c5nr01839k

Kubiak-Ossowska, Karina; Cwieka, Monika; Kaczynska, Agnieszka; Jachimska, Barbara; Mulheran, Paul A.
Lysozyme adsorption at a silica surface using simulation and experiment: effects of pH on protein layer structure
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:24070-24077, 2015
abstract, full text, DOI:10.1039/c5cp03910j

Kucuk, Sami Emre; Biktagirov, Timur; Sezer, Deniz
Carbon and proton Overhauser DNP from MD simulations and ab initio calculations: TEMPOL in acetone
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:24874-24884, 2015
abstract, full text, DOI:10.1039/c5cp04405g

Do, Hainam; Troisi, Alessandro
Developing accurate molecular mechanics force fields for conjugated molecular systems
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:25123-25132, 2015
abstract, full text, DOI:10.1039/c5cp04328j

Jiang, Yafei; Tan, Hongwei; Zheng, Jimin; Li, Xichen; Chen, Guangju; Jia, Zongchao
Phosphoryl transfer reaction catalyzed by membrane diacylglycerol kinase: a theoretical mechanism study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:25228-25234, 2015
abstract, full text, DOI:10.1039/c5cp03342j

Wang, Xiaoqing; Ritschel, Gerhard; Wuester, Sebastian; Eisfeld, Alexander
Open quantum system parameters for light harvesting complexes from molecular dynamics
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:25629-25641, 2015
abstract, full text, DOI:10.1039/c5cp03891j

Das, Amit; Sikdar, Samapan; Ghosh, Mahua; Chakrabarti, J.
Conformational thermodynamics of biomolecular complexes: The histogram-based method
STATPHYS-KOLKATA VIII, 638 Art. No. 012013, 2015
abstract, full text, DOI:10.1088/1742-6596/638/1/012013

Yi, Changhong; Wambo, Thierry O.
Factors affecting the interactions between beta-lactoglobulin and fatty acids as revealed in molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:23074-23080, 2015
abstract, full text, DOI:10.1039/c5cp02312b

Chinnasamy, Sathishkumar; Nagamani, Selvaraman; Muthusamy, Karthikeyan
Zn2+ ion of the snake venom metalloproteinase (SVMP) plays a critical role in ligand binding: a molecular dynamics simulation study
RSC ADVANCES, 5:70566-70576, 2015
abstract, full text, DOI:10.1039/c5ra14693c

Pablo Mendez, Juan; Carlos Zenteno, Juan; Coronel, Agustin; Antonio Soriano-Ursua, Marvin; Yazmin Valencia-Villalvazo, Elith; Soderlund, Daniela; Mauricio Coral-Vazquez, Ramon; Canto, Patricia
Triallelic digenic mutation in the prokineticin 2 and GNRH receptor genes in two brothers with normosmic congenital hypogonadotropic hypogonadism
ENDOCRINE RESEARCH, 40:166-171, 2015
abstract, full text, DOI:10.3109/07435800.2014.982327

Russell, B. A.; Kubiak-Ossowska, K.; Mulheran, P. A.; Birch, D. J. S.; Chen, Y.
Locating the nucleation sites for protein encapsulated gold nanoclusters: a molecular dynamics and fluorescence study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:21935-21941, 2015
abstract, full text, DOI:10.1039/c5cp02380g

Kojic, Milos; Milosevic, Miljan; Wu, Suhong; Blanco, Elvin; Ferrari, Mauro; Ziemys, Arturas
Mass partitioning effects in diffusion transport
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:20630-20635, 2015
abstract, full text, DOI:10.1039/c5cp02720a

Bhunia, Shome S.; Singh, Supriya; Saxena, Shruti; Saxena, Anil K.
Pharmacophore Modeling, Docking and Molecular Dynamics Studies on Caspase-3 Activators Binding at beta-Tubulin Site
CURRENT COMPUTER-AIDED DRUG DESIGN, 11:72-83, 2015
abstract, full text

Bellani, S.; Porro, M.; Caddeo, C.; Saba, M. I.; Miranda, P. B.; Mattoni, A.; Lanzani, G.; Antognazza, M. R.
The study of polythiophene/water interfaces by sum-frequency generation spectroscopy and molecular dynamics simulations
JOURNAL OF MATERIALS CHEMISTRY B, 3:6429-6438, 2015
abstract, full text, DOI:10.1039/c5tb00388a

Araujo, Pedro M. M.; da Silva, Luis Pinto; Esteves da Silva, Joaquim C. G.
Theoretical Analysis of the Binding of Potential Inhibitors to Protein Kinases MK2 and MK3
MEDICINAL CHEMISTRY, 11:573-579, 2015
abstract, full text

Espinoza-Fonseca, L. Michel; Alamo, Lorenzo; Pinto, Antonio; Thomas, David D.; Padron, Raul
Sequential myosin phosphorylation activates tarantula thick filament via a disorder-order transition
MOLECULAR BIOSYSTEMS, 11:2167-2179, 2015
abstract, full text, DOI:10.1039/c5mb00162e

Alamo, Lorenzo; Li, Xiaochuan (Edward); Espinoza-Fonseca, L. Michel; Pinto, Antonio; Thomas, David D.; Lehman, William; Padron, Raul
Tarantula myosin free head regulatory light chain phosphorylation stiffens N-terminal extension, releasing it and blocking its docking back
MOLECULAR BIOSYSTEMS, 11:2180-2189, 2015
abstract, full text, DOI:10.1039/c5mb00163c

Wang, Yanli; Yao, Chenjie; Li, Chenchen; Ding, Lin; Liu, Jian; Dong, Peng; Fang, Haiping; Lei, Zhendong; Shi, Guosheng; Wu, Minghong
Excess titanium dioxide nanoparticles on the cell surface induce cytotoxicity by hindering ion exchange and disrupting exocytosis processes
NANOSCALE, 7:13105-13115, 2015
abstract, full text, DOI:10.1039/c5nr03269e

Alberga, Domenico; Perrier, Aurelie; Ciofini, Ilaria; Mangiatordi, Giuseppe Felice; Lattanzi, Gianluca; Adamo, Carlo
Morphological and charge transport properties of amorphous and crystalline P3HT and PBTTT: insights from theory
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:18742-18750, 2015
abstract, full text, DOI:10.1039/c5cp02769a

Camarada, M. B.; Marquez-Miranda, V.; Araya-Duran, I.; Yevenes, A.; Gonzalez-Nilo, F.
PAMAM G4 dendrimers as inhibitors of the iron storage properties of human L-chain ferritin
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:19001-19011, 2015
abstract, full text, DOI:10.1039/c5cp02594j

Rhinehardt, Kristen L.; Mohan, Ram V.; Srinivas, Goundla
Computational Modeling of Peptide-Aptamer Binding
COMPUTATIONAL PEPTIDOLOGY, 1268:313-333, 2015
abstract, full text, DOI:10.1007/978-1-4939-2285-7_14

Shen, Jia-Wei; Tang, Ting; Wei, Xiao-Hong; Zheng, Wei; Sun, Tian-Yang; Zhang, Zhisen; Liang, Lijun; Wang, Qi
On the loading mechanism of ssDNA into carbon nanotubes
RSC ADVANCES, 5:56896-56903, 2015
abstract, full text, DOI:10.1039/c5ra01941a

Liu, Ying; Chipot, Christophe; Shao, Xueguang; Cai, Wensheng
What causes tumbling of altro-alpha-CD derivatives? Insight from computer simulations
RSC ADVANCES, 5:57309-57317, 2015
abstract, full text, DOI:10.1039/c5ra05642j

Bouvier, Benjamin; Cezard, Christine; Sonnet, Pascal
Selectivity of pyoverdine recognition by the FpvA receptor of Pseudomonas aeruginosa from molecular dynamics simulations
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:18022-18034, 2015
abstract, full text, DOI:10.1039/c5cp02939b

Michino, Mayako; Shi, Lei
Computational Approaches in the Structure-Function Studies of Dopamine Receptors
DOPAMINE RECEPTOR TECHNOLOGIES, 96:31-42, 2015
abstract, full text, DOI:10.1007/978-1-4939-2196-6_3

Pothula, Karunakar Reddy; Kleinekathoefer, Ulrich
Theoretical analysis of ion conductance and gating transitions in the OpdK (OccK1) channel
ANALYST, 140:4855-4864, 2015
abstract, full text, DOI:10.1039/c5an00036j

Espinoza-Fonseca, L. Michel; Kelekar, Ameeta
High-resolution structural characterization of Noxa, an intrinsically disordered protein, by microsecond molecular dynamics simulations
MOLECULAR BIOSYSTEMS, 11:1850-1856, 2015
abstract, full text, DOI:10.1039/c5mb00170f

Tse, A.; Verkhivker, G. M.
Small-world networks of residue interactions in the Abl kinase complexes with cancer drugs: topology of allosteric communication pathways can determine drug resistance effects
MOLECULAR BIOSYSTEMS, 11:2082-2095, 2015
abstract, full text, DOI:10.1039/c5mb00246j

Lu, Yan; Salsbury, Freddie R., Jr.
Recapturing the Correlated Motions of Protein Using Coarse-Grained Models
PROTEIN AND PEPTIDE LETTERS, 22:654-659, 2015
abstract, full text

Kraszewski, Sebastian; Drabik, Dominik; Langner, Marek; Ramseyer, Christophe; Kembubpha, Sineenat; Yasothornsrikul, Sukkid
A molecular dynamics study of catestatin docked on nicotinic acetylcholine receptors to identify amino acids potentially involved in the binding of chromogranin A fragments
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:17454-17460, 2015
abstract, full text, DOI:10.1039/c4cp02491e

Skelton, A. A.; Agrawal, N.; Fried, J. R.
Quantum mechanical calculations of the interactions between diazacrowns and the sodium cation: an insight into Na+ complexation in diazacrown-based synthetic ion channels
RSC ADVANCES, 5:55033-55047, 2015
abstract, full text, DOI:10.1039/c4ra14000a

Penna, M. J.; Mijajlovic, M.; Tamerler, C.; Biggs, M. J.
Molecular-level understanding of the adsorption mechanism of a graphite-binding peptide at the water/graphite interface
SOFT MATTER, 11:5192-5203, 2015
abstract, full text, DOI:10.1039/c5sm00123d

Guo, Song; Xu, Liang; Xu, Kejing; Zhao, Jianzhang; Kucukoz, Betul; Karatay, Ahmet; Yaglioglu, Halime Gul; Hayvali, Mustafa; Elmali, Ayhan
Bodipy-C-60 triple hydrogen bonding assemblies as heavy atom-free triplet photosensitizers: preparation and study of the singlet/triplet energy transfer
CHEMICAL SCIENCE, 6:3724-3737, 2015
abstract, full text, DOI:10.1039/c4sc03865g

Perez-Fuentes, Leonor; Drummond, Carlos; Faraudo, Jordi; Bastos-Gonzalez, Delfi
Anions make the difference: insights from the interaction of big cations and anions with poly(N-isopropylacrylamide) chains and microgels
SOFT MATTER, 11:5077-5086, 2015
abstract, full text, DOI:10.1039/c5sm00750j

Sabbadin, Davide; Ciancetta, Antonella; Deganutti, Giuseppe; Cuzzolin, Alberto; Moro, Stefano
Exploring the recognition pathway at the human A(2A) adenosine receptor of the endogenous agonist adenosine using supervised molecular dynamics simulations
MEDCHEMCOMM, 6:1081-1085, 2015
abstract, full text, DOI:10.1039/c5md00016e

Badu, Shyam; Melnik, Roderick; Prabhakar, Sanjay
Studying Properties of RNA Nanotubes via Molecular Dynamics
NANOSENSORS, BIOSENSORS, AND INFO-TECH SENSORS AND SYSTEMS 2015, 9434 Art. No. 94340E, 2015
abstract, full text, DOI:10.1117/12.2087444

Maity, Sibaprasad; Zanuy, David; Razvag, Yair; Das, Priyadip; Aleman, Carlos; Reches, Meital
Elucidating the mechanism of interaction between peptides and inorganic surfaces
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:15305-15315, 2015
abstract, full text, DOI:10.1039/c5cp00088b

Pall, Szilard; Abraham, Mark James; Kutzner, Carsten; Hess, Berk; Lindahl, Erik
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
SOLVING SOFTWARE CHALLENGES FOR EXASCALE, 8759:3-27, 2015
abstract, full text, DOI:10.1007/978-3-319-15976-8_1

Dixit, Purushottam D.
Detecting temperature fluctuations at equilibrium
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:13000-13005, 2015
abstract, full text, DOI:10.1039/c5cp01423a

Bansode, Sneha B.; Batkulwar, Kedar B.; Warkad, Shrikant D.; Jana, Asis K.; Sengupta, Neelanjana; Kulkarni, Mahesh J.
Tolbutamide induces conformational change and promotes albumin glycation
RSC ADVANCES, 5:40070-40075, 2015
abstract, full text, DOI:10.1039/c5ra03839a

Menon, Sneha; Sengupta, Neelanjana
Perturbations in inter-domain associations may trigger the onset of pathogenic transformations in PrPC: insights from atomistic simulations
MOLECULAR BIOSYSTEMS, 11:1443-1453, 2015
abstract, full text, DOI:10.1039/c4mb00689e

Kucukkal, Tugba G.; Alexov, Emil
Structural, Dynamical, and Energetical Consequences of Rett Syndrome Mutation R133C in MeCP2
COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE, Art. No. 746157, 2015
abstract, full text, DOI:10.1155/2015/746157

Verma, Saroj; Prabhakar, Yenamandra S.
Target Based Drug Design - A Reality in Virtual Sphere
CURRENT MEDICINAL CHEMISTRY, 22:1603-1630, 2015
abstract, full text

Ding, Yun-Qiao; Chen, Cheng-Lung; Li, Tian-Duo; Cheng, Jin-Yong; Zhang, Hua-Yong
Effects of Chromium-olation Length on Crosslinking Effects Investigated by Molecular Dynamics Simulation
SOFT MATERIALS, 13:24-31, 2015
abstract, full text, DOI:10.1080/1539445X.2014.998342

Bochicchio, Brigida; Pepe, Antonietta; Crudele, Maria; Belloy, Nicolas; Baud, Stephanie; Dauchez, Manuel
Tuning self-assembly in elastin-derived peptides
Soft Matter, 11:3385-3395, 2015
abstract, full text, DOI:10.1039/c5sm00072f

Pradeepkiran, Jangampalli Adi; Kumar, Konidala Kranthi; Kumar, Yellapu Nanda; Bhaskar, Matcha
Modeling, molecular dynamics, and docking assessment of transcription factor rho: a potential drug target in Brucella melitensis 16M
DRUG DESIGN DEVELOPMENT AND THERAPY, 9:1897-1912, 2015
abstract, full text, DOI:10.2147/DDDT.S77020

Kelly, Catherine M.; Muzard, Julien; Brooks, Bernard R.; Lee, Gil U.; Buchete, Nicolae-Viorel
Structure and dynamics of the fibronectin-III domains of Aplysia californica cell adhesion molecules
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:9634-9643, 2015
abstract, full text, DOI:10.1039/c4cp05307a

Vitiello, Giuseppe; Falanga, Annarita; Alcides Petruk, Ariel; Merlino, Antonello; Fragneto, Giovanna; Paduano, Luigi; Galdiero, Stefania; D'Errico, Gerardino
Fusion of raft-like lipid bilayers operated by a membranotropic domain of the HSV-type I glycoprotein gH occurs through a cholesterol-dependent mechanism
SOFT MATTER, 11:3003-3016, 2015
abstract, full text, DOI:10.1039/c4sm02769h

Mintzer, Mary Rose; Troxler, Thomas; Gai, Feng
p-Cyanophenylalanine and selenomethionine constitute a useful fluorophore-quencher pair for short distance measurements: application to polyproline peptides
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:7881-7887, 2015
abstract, full text, DOI:10.1039/c5cp00050e

Basu, Ipsita; Mukhopadhyay, Chaitali
Effect of Temperature on the Phase Behaviour of Fully Saturated DAPC Lipid Bilayer: A Comparative Molecular Dynamics Simulation Study
BIOCHEMICAL ROLES OF EUKARYOTIC CELL SURFACE MACROMOLECULES, 842:263-277, 2015
full text

Abroshan, Hadi; Kim, Hyung J.
On the structural stability of ionic liquid-IRMOF composites: a computational study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:6248-6254, 2015
abstract, full text, DOI:10.1039/c4cp02428a

Kucuk, Sami Emre; Neugebauer, Petr; Prisner, Thomas F.; Sezer, Deniz
Molecular simulations for dynamic nuclear polarization in liquids: a case study of TEMPOL in acetone and DMSO
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:6618-6628, 2015
abstract, full text, DOI:10.1039/c4cp05832a

Azamat, Jafar; Khataee, Alireza; Joo, Sang Woo
Removal of heavy metals from water through armchair carbon and boron nitride nanotubes: a computer simulation study
RSC ADVANCES, 5:25097-25104, 2015
abstract, full text, DOI:10.1039/c4ra17048b

Insaidoo, Francis K.; Rauscher, Michael A.; Smithline, Shepard J.; Kaarsholm, Niels C.; Feuston, Bradley P.; Ortigosa, Allison D.; Linden, Thomas O.; Roush, David J.
Targeted Purification Development Enabled by Computational Biophysical Modeling
BIOTECHNOLOGY PROGRESS, 31:154-164, JAN-FEB 2015
abstract, full text, DOI:10.1002/btpr.2023

Duarte Junior, Francisco Ferreira; de Lima Neto, Quirino Alves; Rando, Fabiana dos Santos; Bassalobre de Freitas, Douglas Vinicius; Pattaro Junior, Jose Renato; Polizelli, Lorena Gomes; Ferreira Munhoz, Roxelle Ethienne; Vicente Seixas, Flavio Augusto; Fernandez, Maria Aparecida
Identification and molecular structure analysis of a new noncoding RNA, a sbRNA homolog, in the silkworm Bombyx mori genome
MOLECULAR BIOSYSTEMS, 11:801-808, 2015
abstract, full text, DOI:10.1039/c4mb00595c

Li, Hui; Chen, Qi; Schoenbeck, Christian; Han, Bao-Hang
Sugar-functionalized water-soluble pillar[5] arene and its host-guest interaction with fullerene
RSC ADVANCES, 5:19041-19047, 2015
abstract, full text, DOI:10.1039/c4ra07523d

Alishahi, Marzieh; Kamali, Reza; Abouali, Omid
Molecular Dynamics Study of Electric Double Layer in Nanochannel
RUSSIAN JOURNAL OF ELECTROCHEMISTRY, 51:49-55, JAN 2015
abstract, full text, DOI:10.1134/S1023193515010024

Gonnet, Pedro
EFFICIENT AND SCALABLE ALGORITHMS FOR SMOOTHED PARTICLE HYDRODYNAMICS ON HYBRID SHARED/DISTRIBUTED-MEMORY ARCHITECTURES
SIAM JOURNAL ON SCIENTIFIC COMPUTING, 37:C95-C121, 2015
abstract, full text, DOI:10.1137/140964266

Kumar, Amit; Sechi, Leonardo A.; Caboni, Pierluigi; Marrosu, Maria Giovanna; Atzori, Luigi; Pieroni, Enrico
Dynamical insights into the differential characteristics of Mycobacterium avium subsp paratuberculosis peptide binding to HLA-DRB1 proteins associated with multiple sclerosis
NEW JOURNAL OF CHEMISTRY, 39:1355-1366, 2015
abstract, full text, DOI:10.1039/c4nj01903b

Grimes, Leanne; Young, Mark T.
Purinergic P2X Receptors: Structural and Functional Features Depicted by X-Ray and Molecular Modelling Studies
CURRENT MEDICINAL CHEMISTRY, 22:783-798, 2015
abstract, full text

Dean, Kevin M.; Lubbeck, Jennifer L.; Davis, Lloyd M.; Regmi, Chola K.; Chapagain, Prem P.; Gerstman, Bernard S.; Jimenez, Ralph; Palmer, Amy E.
Microfluidics-based selection of red-fluorescent proteins with decreased rates of photobleaching
INTEGRATIVE BIOLOGY, 7:263-273, 2015
abstract, full text, DOI:10.1039/c4ib00251b

Wessel, Jennifer; Chu, Audrey Y.; Willems, Sara M.; Wang, Shuai; Yaghootkar, Hanieh; Brody, Jennifer A.; Dauriz, Marco; Hivert, Marie-France; Raghavan, Sridharan; Lipovich, Leonard; Hidalgo, Bertha; Fox, Keolu; Huffman, Jennifer E.; An, Ping; Lu, Yingchang; Rasmussen-Torvik, Laura J.; Grarup, Niels; Ehm, Margaret G.; Li, Li; Baldridge, Abigail S.; Stancakova, Alena; Abrol, Ravinder; Besse, Celine; Boland, Anne; Bork-Jensen, Jette; Fornage, Myriam; Freitag, Daniel F.; Garcia, Melissa E.; Guo, Xiuqing; Hara, Kazuo; Isaacs, Aaron; Jakobsdottir, Johanna; Lange, Leslie A.; Layton, Jill C.; Li, Man; Zhao, Jing Hua; Meidtner, Karina; Morrison, Alanna C.; Nalls, Mike A.; Peters, Marjolein J.; Sabater-Lleal, Maria; Schurmann, Claudia; Silveira, Angela; Smith, Albert V.; Southam, Lorraine; Stoiber, Marcus H.; Strawbridge, Rona J.; Taylor, Kent D.; Varga, Tibor V.; Allin, Kristine H.; Amin, Najaf; Aponte, Jennifer L.; Aung, Tin; Barbieri, Caterina; Bihlmeyer, Nathan A.; Boehnke, Michael; Bombieri, Cristina; Bowden, Donald W.; Burns, Sean M.; Chen, Yuning; Chen, Yii-Deri; Cheng, Ching-Yu; Correa, Adolfo; Czajkowski, Jacek; Dehghan, Abbas; Ehret, Georg B.; Eiriksdottir, Gudny; Escher, Stefan A.; Farmaki, Aliki-Eleni; Franberg, Mattias; Gambaro, Giovanni; Giulianini, Franco; Goddard, William A., I.I.I.; Goel, Anuj; Gottesman, Omri; Grove, Megan L.; Gustafsson, Stefan; Hai, Yang; Hallmans, Goeran; Heo, Jiyoung; Hoffmann, Per; Ikram, Mohammad K.; Jensen, Richard A.; Jorgensen, Marit E.; Jorgensen, Torben; Karaleftheri, Maria; Khor, Chiea C.; Kirkpatrick, Andrea; Kraja, Aldi T.; Kuusisto, Johanna; Lange, Ethan M.; Lee, I. T.; Lee, Wen-Jane; Leong, Aaron; Liao, Jiemin; Liu, Chunyu; Liu, Yongmei; Lindgren, Cecilia M.; Linneberg, Allan; Malerba, Giovanni; Mamakou, Vasiliki; Marouli, Eirini; Maruthur, Nisa M.; Matchan, Angela; McKean-Cowdin, Roberta; McLeod, Olga; Metcalf, Ginger A.; Mohlke, Karen L.; Muzny, Donna M.; Ntalla, Ioanna; Palmer, Nicholette D.; Pasko, Dorota; Peter, Andreas; Rayner, Nigel W.; Renstroem, Frida; Rice, Ken; Sala, Cinzia F.; Sennblad, Bengt; Serafetinidis, Ioannis; Smith, Jennifer A.; Soranzo, Nicole; Speliotes, Elizabeth K.; Stahl, Eli A.; Stirrups, Kathleen; Tentolouris, Nikos; Thanopoulou, Anastasia; Torres, Mina; Traglia, Michela; Tsafantakis, Emmanouil; Javad, Sundas; Yanek, Lisa R.; Zengini, Eleni; Becker, Diane M.; Bis, Joshua C.; Brown, James B.; Cupples, L. Adrienne; Hansen, Torben; Ingelsson, Erik; Karter, Andrew J.; Lorenzo, Carlos; Mathias, Rasika A.; Norris, Jill M.; Peloso, Gina M.; Sheu, Wayne H. -H.; Toniolo, Daniela; Vaidya, Dhananjay; Varma, Rohit; Wagenknecht, Lynne E.; Boeing, Heiner; Bottinger, Erwin P.; Dedoussis, George; Deloukas, Panos; Ferrannini, Ele; Franco, Oscar H.; Franks, Paul W.; Gibbs, Richard A.; Gudnason, Vilmundur; Hamsten, Anders; Harris, Tamara B.; Hattersley, Andrew T.; Hayward, Caroline; Hofman, Albert; Jansson, Jan-Hakan; Langenberg, Claudia; Launer, Lenore J.; Levy, Daniel; Oostra, Ben A.; O'Donnell, Christopher J.; O'Rahilly, Stephen; Padmanabhan, Sandosh; Pankow, James S.; Polasek, Ozren; Province, Michael A.; Rich, Stephen S.; Ridker, Paul M.; Rudan, Igor; Schulze, Matthias B.; Smith, Blair H.; Uitterlinden, Andre G.; Walker, Mark; Watkins, Hugh; Wong, Tien Y.; Zeggini, Eleftheria; Laakso, Markku; Borecki, Ingrid B.; Chasman, Daniel I.; Pedersen, Oluf; Psaty, Bruce M.; Tai, E. Shyong; van Duijn, Cornelia M.; Wareham, Nicholas J.; Waterworth, Dawn M.; Boerwinkle, Eric; Kao, W. H. Linda; Florez, Jose C.; Loos, Ruth J. F.; Wilson, James G.; Frayling, Timothy M.; Siscovick, David S.; Dupuis, Josee; Rotter, Jerome I.; Meigs, James B.; Scott, Robert A.; Goodarzi, Mark O.; Sharp, Stephen J.; Forouhi, Nita G.; Kerrison, Nicola D.; Lucarelli, Debora M. E.; Sims, Matt; Barroso, Ines; McCarthy, Mark I.; Arriola, Larraitz; Balkau, Beverley; Barricarte, Aurelio; Gonzalez, Carlos; Grioni, Sara; Kaaks, Rudolf; Key, Timothy J.; Navarro, Carmen; Nilsson, Peter M.; Overvad, Kim; Palli, Domenico; Panico, Salvatore; Quiros, J. Ramon; Rolandsson, Olov; Sacerdote, Carlotta; Sanchez, Maria-Jose; Slimani, Nadia; Tjonneland, Anne; Tumino, Rosario; van der A, Daphne L.; van der Schouw, Yvonne T.; Riboli, Elio
Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility
NATURE COMMUNICATIONS, 6 Art. No. 5897, JAN 2015
abstract, full text, DOI:10.1038/ncomms6897

Luan, Binquan; Tien Huynh; Zhao, Lin; Zhou, Ruhong
Potential Toxicity of Graphene to Cell Functions via Disrupting Protein-Protein Interactions
ACS NANO, 9:663-669, JAN 2015
abstract, full text, DOI:10.1021/nn506011j

Cheng, Bo; Wu, Shaogui; Liu, Shixin; Rodriguez-Aliaga, Piere; Yu, Jin; Cui, Shuxun
Protein denaturation at a single-molecule level: the effect of nonpolar environments and its implications on the unfolding mechanism by proteases
NANOSCALE, 7:2970-2977, 2015
abstract, full text, DOI:10.1039/c4nr07140a

Nichols, Pilarin; Li, Li; Kumar, Sandeep; Buck, Patrick M.; Singh, Satish K.; Goswami, Sumit; Balthazor, Bryan; Conley, Tami R.; Sek, David; Allen, Martin J.
Rational design of viscosity reducing mutants of a monoclonal antibody: Hydrophobic versus electrostatic inter-molecular interactions
MABS, 7:212-230, JAN-FEB 2015
abstract, full text, DOI:10.4161/19420862.2014.985504

Danishuddin, Mohd; Khan, Asad U.
Structure based virtual screening to discover putative drug candidates: Necessary considerations and successful case studies
METHODS, 71:135-145, JAN 1 2015
abstract, full text, DOI:10.1016/j.ymeth.2014.10.019

Rakos, Balazs
Modeling of dipole-dipole-coupled, electric field-driven, protein-based computing architectures
INTERNATIONAL JOURNAL OF CIRCUIT THEORY AND APPLICATIONS, 43:60-72, JAN 2015
abstract, full text, DOI:10.1002/cta.1924

Ferrarotti, Marco Jacopo; Bottaro, Sandro; Perez-Villa, Andrea; Bussi, Giovanni
Accurate Multiple Time Step in Biased Molecular Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:139-146, JAN 2015
abstract, full text, DOI:10.1021/ct5007086

Cordova-Mateo, Esther; Bertran, Oscar; Schlueter, A. Dieter; Kroeger, Martin; Aleman, Carlos
Internal organization of macromonomers and dendronized polymers based on thiophene dendrons
SOFT MATTER, 11:1116-1126, 2015
abstract, full text, DOI:10.1039/c4sm02523g

Gray, Alan; Harlen, Oliver G.; Harris, Sarah A.; Khalid, Syma; Leung, Yuk Ming; Lonsdale, Richard; Mulholland, Adrian J.; Pearson, Arwen R.; Read, Daniel J.; Richardson, Robin A.
In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 71:162-172, JAN 2015
abstract, full text, DOI:10.1107/S1399004714026777

Schulz, Robert; Vargiu, Attilio V.; Ruggerone, Paolo; Kleinekathoefer, Ulrich
Computational Study of Correlated Domain Motions in the AcrB Efflux Transporter
BIOMED RESEARCH INTERNATIONAL, Art. No. 487298, 2015
abstract, full text, DOI:10.1155/2015/487298

Decherchi, Sergio; Berteotti, Anna; Bottegoni, Giovanni; Rocchia, Walter; Cavalli, Andrea
The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning
Nature Communications, 6 Art. No. 6155, JAN 2015
abstract, full text, DOI:10.1038/ncomms7155

Lu Shi-Jing; Zhou Xin
Construction of Coarse-Grained Models by Reproducing Equilibrium Probability Density Function
COMMUNICATIONS IN THEORETICAL PHYSICS, 63:10-18, JAN 2015
abstract, full text

Rocca, Roberta; Moraca, Federica; Costa, Giosue; Alcaro, Stefano; Distinto, Simona; Maccioni, Elias; Ortuso, Francesco; Artese, Anna; Parrotta, Lucia
Structure-Based Virtual Screening of Novel Natural Alkaloid Derivatives as Potential Binders of h-telo and c-myc DNA G-Quadruplex Conformations
MOLECULES, 20:206-223, JAN 2015
abstract, full text, DOI:10.3390/molecules20010206

Wineman-Fisher, Vered; Atsmon-Raz, Yoav; Miller, Yifat
Orientations of Residues along the beta-Arch of Self-Assembled Amylin Fibril-Like Structures Lead to Polymorphism
BIOMACROMOLECULES, 16:156-165, JAN 2015
abstract, full text, DOI:10.1021/bm501326y

Rovira, Xavier; Malhaire, Fanny; Scholler, Pauline; Rodrigo, Jordi; Gonzalez-Bulnes, Patricia; Llebaria, Amadeu; Pin, Jean-Philippe; Giraldo, Jesus; Goudet, Cyril
Overlapping binding sites drive allosteric agonism and positive cooperativity in type 4 metabotropic glutamate receptors
FASEB JOURNAL, 29:116-130, JAN 2015
abstract, full text, DOI:10.1096/fj.14-257287

Gerbier, Romain; Leroux, Vincent; Couvineau, Pierre; Alvear-Perez, Rodrigo; Maigret, Bernard; Llorens-Cortes, Catherine; Iturrioz, Xavier
New structural insights into the apelin receptor: identification of key residues for apelin binding
FASEB JOURNAL, 29:314-322, JAN 2015
abstract, full text, DOI:10.1096/fj.14-256339

Katti, Dinesh R.; Sharma, Anurag; Ambre, Avinash H.; Katti, Kalpana S.
Molecular interactions in biomineralized hydroxyapatite amino acid modified nanoclay: In silico design of bone biomaterials
MATERIALS SCIENCE & ENGINEERING C-MATERIALS FOR BIOLOGICAL APPLICATIONS, 46:207-217, JAN 1 2015
abstract, full text, DOI:10.1016/j.msec.2014.07.057

Fraiberg, Milana; Afanzar, Oshri; Cassidy, C. Keith; Gabashvili, Alexandra; Schulten, Klaus; Levin, Yishai; Eisenbach, Michael
CheY's acetylation sites responsible for generating clockwise flagellar rotation in Escherichia coli
MOLECULAR MICROBIOLOGY, 95:231-244, JAN 2015
abstract, full text, TCBG publications, DOI:10.1111/mmi.12858

Wu, Wenyun; Yue, Jingying; Li, Dongqi; Lin, Xiaoyang; Zhu, Fangqiang; Yin, Xue; Zhu, Jun; Dai, Xingcan; Liu, Peng; Wei, Yang; Wang, Jiaping; Yang, Haitao; Zhang, Lina; Li, Qunqing; Fan, Shoushan; Jiang, Kaili
Interface dipole enhancement effect and enhanced Rayleigh scattering
NANO RESEARCH, 8:303-319, JAN 2015
abstract, full text, DOI:10.1007/s12274-014-0687-5

Xu, Lei; Li, Youyong; Li, Dan; Xu, Peng; Tian, Sheng; Sun, Huiyong; Liu, Hui; Hou, Tingjun
Exploring the binding mechanisms of MIF to CXCR2 using theoretical approaches
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:3370-3382, 2015
abstract, full text, DOI:10.1039/c4cp05095a

Villarreal, Oscar D.; Chen, Liao Y.; Whetten, Robert L.; Yacaman, Miguel J.
Ligand-modulated interactions between charged monolayer-protected Au-144(SR)(60) gold nanoparticles in physiological saline
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:3680-3688, 2015
abstract, full text, DOI:10.1039/c4cp05137h

Gupta, Kushol; Selinsky, Barry S.
Bacterial and algal orthologs of prostaglandin H-2 synthase: novel insights into the evolution of an integral membrane protein
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1848:83-94, JAN 2015
abstract, full text, DOI:10.1016/j.bbamem.2014.09.011

Carrasquel-Ursulaez, Willy; Contreras, Gustavo F.; Sepulveda, Romina V.; Aguayo, Daniel; Gonzalez-Nilo, Fernando; Gonzalez, Carlos; Latorre, Ramon
Hydrophobic interaction between contiguous residues in the S6 transmembrane segment acts as a stimuli integration node in the BK channel
JOURNAL OF GENERAL PHYSIOLOGY, 145:61-74, JAN 2015
abstract, full text, DOI:10.1085/jgp.201411194

Rodriguez-Rodriguez, C.; Telpoukhovskaia, M. A.; Ali-Torres, J.; Rodriguez-Santiago, L.; Manso, Y.; Bailey, G. A.; Hidalgo, J.; Sodupe, M.; Orvig, C.
Thioflavin-based molecular probes for application in Alzheimer's disease: from in silico to in vitro models
METALLOMICS, 7:78-87, 2015
abstract, full text, DOI:10.1039/c4mt00167b

Kalimeri, Maria; Derreumaux, Philippe; Sterpone, Fabio
Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field
JOURNAL OF NON-CRYSTALLINE SOLIDS, 407:494-501, JAN 1 2015
abstract, full text, DOI:10.1016/j.jnoncrysol.2014.07.005

Ruiz, Luis; Wu, Yuanqiao; Keten, Sinan
Tailoring the water structure and transport in nanotubes with tunable interiors
NANOSCALE, 7:121-132, 2015
abstract, full text, DOI:10.1039/c4nr05407e

Leman, Julia Koehler; Ulmschneider, Martin B.; Gray, Jeffrey J.
Computational modeling of membrane proteins
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:1-24, JAN 2015
abstract, full text, DOI:10.1002/prot.24703

Ng, Yao Zong; Kannan, Srinivasaraghavan; Lane, David P.; Fuentes, Gloria; Verma, Chandra S.
mAb806 binding to epidermal growth factor receptor: a computational study
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 83:153-168, JAN 2015
abstract, full text, DOI:10.1002/prot.24714

Sule, Nitesh V.; Ugrinov, Angel; Mallik, Sanku; Srivastava, D. K.
Bridging of a substrate between cyclodextrin and an enzyme's active site pocket triggers a unique mode of inhibition
BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, 1850:141-149, JAN 2015
abstract, full text, DOI:10.1016/j.bbagen.2014.10.016

Choi, Bumjoon; Yoon, Gwonchan; Lee, Sang Woo; Eom, Kilho
Mechanical deformation mechanisms and properties of amyloid fibrils
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:1379-1389, 2015
abstract, full text, DOI:10.1039/c4cp03804e

Nierzwicki, L.; Wieczor, M.; Censi, V.; Baginski, M.; Calucci, L.; Samaritani, S.; Czub, J.; Forte, C.
Interaction of cisplatin and two potential antitumoral platinum(II) complexes with a model lipid membrane: a combined NMR and MD study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:1458-1468, 2015
abstract, full text, DOI:10.1039/c4cp04360j

Agosta, Lorenzo; Zollo, Giuseppe; Arcangeli, Caterina; Buonocore, Francesco; Gala, Fabrizio; Celino, Massimo
Water driven adsorption of amino acids on the (101) anatase TiO2 surface: an ab initio study
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:1556-1561, 2015
abstract, full text, DOI:10.1039/c4cp03056g

Culleton, Bridget A.; Lall, Patrick; Kinsella, Gemma K.; Doyle, Sean; McCaffrey, John; Fitzpatrick, David A.; Burnell, Ann M.
A role for the Parkinson's disease protein DJ-1 as a chaperone and antioxidant in the anhydrobiotic nematode Panagrolaimus superbus
CELL STRESS & CHAPERONES, 20:121-137, JAN 2015
abstract, full text, DOI:10.1007/s12192-014-0531-6

Wang, Feng; Wan, Hua; Hu, Jian-ping; Chang, Shan
Molecular dynamics simulations of wild type and mutants of botulinum neurotoxin A complexed with synaptic vesicle protein 2C
MOLECULAR BIOSYSTEMS, 11:223-231, JAN 2015
abstract, full text, DOI:10.1039/c4mb00383g

Carmona, Christopher; Langan, Paul; Smith, Jeremy C.; Petridis, Loukas
Why genetic modification of lignin leads to low-recalcitrance biomass
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17:358-364, 2015
abstract, full text, DOI:10.1039/c4cp05004e

Sun, Yeping; Liu, Qian
Differential structural dynamics and antigenicity of two similar influenza H5N1 virus HA-specific HLA-A*0201-restricted CLT epitopes
RSC ADVANCES, 5:2318-2327, 2015
abstract, full text, DOI:10.1039/c4ra08874c

Pan, Jianjun; Cheng, Xiaolin; Sharp, Melissa; Ho, Chian-Sing; Khadka, Nawal; Katsaras, John
Structural and mechanical properties of cardiolipin lipid bilayers determined using neutron spin echo, small angle neutron and X-ray scattering, and molecular dynamics simulations
SOFT MATTER, 11:130-138, 2015
abstract, full text, DOI:10.1039/c4sm02227k

Jana, Asis K.; Sengupta, Neelanjana
A beta self-association and adsorption on a hydrophobic nanosurface: competitive effects and the detection of small oligomers via electrical response
SOFT MATTER, 11:269-279, 2015
abstract, full text, DOI:10.1039/c4sm01845a

Palese, Luigi Leonardo
Random Matrix Theory in molecular dynamics analysis
BIOPHYSICAL CHEMISTRY, 196:1-9, JAN 2015
abstract, full text, DOI:10.1016/j.bpc.2014.08.007

Kelly, Catherine M.; Northey, Thomas; Ryan, Kate; Brooks, Bernard R.; Kholkin, Andrei L.; Rodriguez, Brian J.; Buchete, Nicolae-Viorel
Conformational dynamics and aggregation behavior of piezoelectric diphenylalanine peptides in an external electric field
BIOPHYSICAL CHEMISTRY, 196:16-24, JAN 2015
abstract, full text, DOI:10.1016/j.bpc.2014.08.009

Sheikh, Sonia; Blaszykowski, Christophe; Nolan, Robert; Thompson, Damien; Thompson, Michael
On the hydration of subnanometric antifouling organosilane adlayers: A molecular dynamics simulation
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 437:197-204, JAN 1 2015
abstract, full text, DOI:10.1016/j.jcis.2014.09.025

Araujo, Pedro M. M.; da Silva, Luis Pinto; Esteves da Silva, Joaquim C. G.
Theoretical Modelling of Potential Chk1 Inhibitors
LETTERS IN DRUG DESIGN & DISCOVERY, 12:60-65, 2015
abstract, full text

Bal, Naresh C.; Jena, Nivedita; Chakravarty, Harapriya; Kumar, Amit; Chi, Mei; Balaraju, Tuniki; Rawale, Sharad V.; Rawale, Jayashree S.; Sharon, Ashoke; Periasamy, Muthu
The C-Terminal Calcium-Sensitive Disordered Motifs Regulate Isoform-Specific Polymerization Characteristics of Calsequestrin
BIOPOLYMERS, 103:15-22, JAN 2015
abstract, full text, DOI:10.1002/bip.22534

Lindahl, Erik
Molecular Dynamics Simulations
MOLECULAR MODELING OF PROTEINS: 2ND EDITION, 1215:3-26, 2015
abstract, full text, DOI:10.1007/978-1-4939-1465-4_1

Biggin, Philip C.; Bond, Peter J.
Molecular Dynamics Simulations of Membrane Proteins
MOLECULAR MODELING OF PROTEINS: 2ND EDITION, 1215:91-108, 2015
abstract, full text, DOI:10.1007/978-1-4939-1465-4_5

Gedeon, Patrick C.; Thomas, James R.; Madura, Jeffry D.
Accelerated Molecular Dynamics and Protein Conformational Change: A Theoretical and Practical Guide Using a Membrane Embedded Model Neurotransmitter Transporter
MOLECULAR MODELING OF PROTEINS: 2ND EDITION, 1215:253-287, 2015
abstract, full text, DOI:10.1007/978-1-4939-1465-4_12

Sorensen, Jesper; Demir, Oezlem; Swift, Robert V.; Feher, Victoria A.; Amaro, Rommie E.
Molecular Docking to Flexible Targets
MOLECULAR MODELING OF PROTEINS: 2ND EDITION, 1215:445-469, 2015
abstract, full text, DOI:10.1007/978-1-4939-1465-4_20

Fossepre, Mathieu; Leherte, Laurence; Laaksonen, Aatto; Vercauteren, Daniel P.
On the Modularity of the Intrinsic Flexibility of the mu Opioid Receptor: A Computational Study
PLOS ONE, 9 Art. No. e115856, DEC 30 2014
abstract, full text, DOI:10.1371/journal.pone.0115856

Fichna, Jakub Piotr; Karolczak, Justyna; Potulska-Chromik, Anna; Miszta, Przemyslaw; Berdynski, Mariusz; Sikorska, Agata; Filipek, Slawomir; Redowicz, Maria Jolanta; Kaminska, Anna; Zekanowski, Cezary
Two Desmin Gene Mutations Associated with Myofibrillar Myopathies in Polish Families
PLOS ONE, 9 Art. No. UNSP e115470, DEC 26 2014
abstract, full text, DOI:10.1371/journal.pone.0115470

Spata, Vincent A.; Matsika, Spiridoula
Role of Excitonic Coupling and Charge-Transfer States in the Absorption and CD Spectra of Adenine-Based Oligonucleotides Investigated through QM/MM Simulations
JOURNAL OF PHYSICAL CHEMISTRY A, 118:12021-12030, DEC 25 2014
abstract, full text, DOI:10.1021/jp507520c

Wang, Nuo; Zhou, Shenggao; Kekenes-Huskey, Peter M.; Li, Bo; McCammon, J. Andrew
Poisson-Boltzmann versus Size-Modified Poisson-Boltzmann Electrostatics Applied to Lipid Bilayers
JOURNAL OF PHYSICAL CHEMISTRY B, 118:14827-14832, DEC 25 2014
abstract, full text, DOI:10.1021/jp511702w

Raczynski, Przemyslaw; Gorny, Krzysztof; Samios, Jannis; Gburski, Zygmunt
Interaction Between Silicon-Carbide Nanotube and Cholesterol Domain. A Molecular Dynamics Simulation Study.
JOURNAL OF PHYSICAL CHEMISTRY C, 118:30115-30119, DEC 25 2014
abstract, full text, DOI:10.1021/jp505532f

Basu, Ipsita; Multhopadhyay, Chaitali
Insights into Binding of Cholera Toxin to GM1 Containing Membrane
LANGMUIR, 30:15244-15252, DEC 23 2014
abstract, full text, DOI:10.1021/la5036618

Karatasos, Kostas
Graphene/Hyperbranched Polymer Nanocomposites: Insight from Molecular Dynamics Simulations
MACROMOLECULES, 47:8833-8845, DEC 23 2014
abstract, full text, DOI:10.1021/ma502123a

Re, Suyong; Nishima, Wataru; Tahara, Tahei; Sugita, Yuji
Mosaic of Water Orientation Structures at a Neutral Zwitterionic Lipid/Water Interface Revealed by Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY LETTERS, 5:4343-4348, DEC 18 2014
abstract, full text, DOI:10.1021/jz502299m

Pujato, Mario; Kieken, Fabien; Skiles, Amanda A.; Tapinos, Nikos; Fiser, Andras
Prediction of DNA binding motifs from 3D models of transcription factors; identifying TLX3 regulated genes
NUCLEIC ACIDS RESEARCH, 42:13500-13512, DEC 16 2014
abstract, full text, DOI:10.1093/nar/gku1228

Marinelli, Fabrizio; Almagor, Lior; Hiller, Reuben; Giladi, Moshe; Khananshvili, Daniel; Faraldo-Gomez, Jose D.
Sodium recognition by the Na+/Ca2+ exchanger in the outward-facing conformation
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:E5354-E5362, DEC 16 2014
abstract, full text, DOI:10.1073/pnas.1415751111

Fuerst, Oliver; Nichols, Colin G.; Lamoureux, Guillaume; D'Avanzo, Nazzareno
Identification of a Cholesterol-Binding Pocket in Inward Rectifier K+ (Kir) Channels
BIOPHYSICAL JOURNAL, 107:2786-2796, DEC 16 2014
abstract, full text, DOI:10.1016/j.bpj.2014.10.066

Lopez-Emparan, Ada; Quezada-Martinez, Daniela; Zuniga-Bustos, Matias; Cifuentes, Victor; Iniguez-Luy, Federico; Laura Federico, Maria
Functional Analysis of the Brassica napus L. Phytoene Synthase (PSY) Gene Family
PLOS ONE, 9 Art. No. e114878, DEC 15 2014
abstract, full text, DOI:10.1371/journal.pone.0114878

Sinko, Robert; Keten, Sinan
Effect of moisture on the traction-separation behavior of cellulose nanocrystal interfaces
APPLIED PHYSICS LETTERS, 105 Art. No. 243702, DEC 15 2014
abstract, full text, DOI:10.1063/1.4904708

Naddaf, Lamis; Sayyed-Ahmad, Abdallah
Intracellular crowding effects on the self-association of the bacterial cell division protein FtsZ
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 564:12-19, DEC 15 2014
abstract, full text, DOI:10.1016/j.abb.2014.08.016

Huang, Zhehao; Yao, Yuan; Han, Lu; Che, Shunai
Control of Chiral Nanostructures by Self-Assembly of Designed Amphiphilic Peptides and Silica Biomineralization
CHEMISTRY-A EUROPEAN JOURNAL, 20:17068-17076, DEC 15 2014
abstract, full text, DOI:10.1002/chem.201403498

Zhou, Yuan-Wu; Liu, Jin-Long; Yu, Zu-Guo; Zhao, Ni Qin; Anh, Vo
Fractal and complex network analyses of protein molecular dynamics
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS, 416:21-32, DEC 15 2014
abstract, full text, DOI:10.1016/j.physa.2014.08.047

Duboue-Dijon, Elise; Laage, Damien
Comparative study of hydration shell dynamics around a hyperactive antifreeze protein and around ubiquitin
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D529, DEC 14 2014
abstract, full text, DOI:10.1063/1.4902822

Harris, Robert C.; Drake, Justin A.; Pettitt, B. Montgomery
Multibody correlations in the hydrophobic solvation of glycine peptides
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D525, DEC 14 2014
abstract, full text, DOI:10.1063/1.4901886

Martinez, Anna Victoria; Malolepsza, Edyta; Rivera, Eva; Lu, Qing; Straub, John E.
Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides A beta(16-22) and Sup35(7-13) in AOT reverse micelles
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D530, DEC 14 2014
abstract, full text, DOI:10.1063/1.4902550

Sharp, Kim A.
The remarkable hydration of the antifreeze protein Maxi: A computational study
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D510, DEC 14 2014
abstract, full text, DOI:10.1063/1.4896693

Sinha, Sudipta Kumar; Jana, Madhurima; Chakraborty, Kausik; Bandyopadhyay, Sanjoy
In silico studies of the properties of water hydrating a small protein
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D502, DEC 14 2014
abstract, full text, DOI:10.1063/1.4895533

Sode, Olaseni; Voth, Gregory A.
Electron transfer activation of a second water channel for proton transport in [FeFe]-hydrogenase
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D527, DEC 14 2014
abstract, full text, DOI:10.1063/1.4902236

Vaitheeswaran, S.; Thirumalai, D.
Entropy and enthalpy of interaction between amino acid side chains in nanopores
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D523, DEC 14 2014
abstract, full text, DOI:10.1063/1.4901204

Virtanen, J. J.; Sosnick, T. R.; Freed, K. F.
Ionic strength independence of charge distributions in solvation of biomolecules
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D503, DEC 14 2014
abstract, full text, DOI:10.1063/1.4895522

Wilson, Michael A.; Thuy Hien Nguyen; Pohorille, Andrew
Combining molecular dynamics and an electrodiffusion model to calculate ion channel conductance
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 22D519, DEC 14 2014
abstract, full text, DOI:10.1063/1.4900879

Morishita, Masayo; Mevius, Damiaan; di Luccio, Eric
In vitro histone lysine methylation by NSD1, NSD2/MMSET/WHSC1 and NSD3/WHSC1L
BMC STRUCTURAL BIOLOGY, 14 Art. No. 25, DEC 12 2014
abstract, full text, DOI:10.1186/s12900-014-0025-x

Migliori, Amy D.; Smith, Douglas E.; Arya, Gaurav
Molecular Interactions and Residues Involved in Force Generation in the T4 Viral DNA Packaging Motor
JOURNAL OF MOLECULAR BIOLOGY, 426:4002-4017, DEC 12 2014
abstract, full text, DOI:10.1016/j.jmb.2014.09.023

Nategholeslam, Mostafa; Gray, C. G.; Tomberli, Bruno
Implementation of the Forward-Reverse Method for Calculating the Potential of Mean Force Using a Dynamic Restraining Protocol
JOURNAL OF PHYSICAL CHEMISTRY B, 118:14203-14214, DEC 11 2014
abstract, full text, DOI:10.1021/jp504942t

Weng, Lindong; Elliott, Gloria D.
Polymerization Effect of Electrolytes on Hydrogen-Bonding Cryoprotectants: Ion-Dipole Interactions between Metal Ions and Glycerol
JOURNAL OF PHYSICAL CHEMISTRY B, 118:14546-14554, DEC 11 2014
abstract, full text, DOI:10.1021/jp5105533

Fenley, Andrew T.; Muddana, Hari S.; Gilson, Michael K.
Calculation and Visualization of Atomistic Mechanical Stresses in Nanomaterials and Biomolecules
PLOS ONE, 9 Art. No. e113119, DEC 11 2014
abstract, full text, DOI:10.1371/journal.pone.0113119

Dwyer, Patrick J.; Vander Valk, Rory J.; Caltaldo, Vito; Dennanicz, David; Keite, Stephen P.
All-Atom CHARMM Force Field and Bulk Properties of Perfluorozinc Phthalocyanines
JOURNAL OF PHYSICAL CHEMISTRY A, 118:11583-11590, DEC 11 2014
abstract, full text, DOI:10.1021/jp506601e

Segrest, Jere P.; Jones, Martin K.; Shao, Baohai; Heinecke, Jay W.
An Experimentally Robust Model of Monomeric Apolipoprotein A-I Created from a Chimera of Two X-ray Structures and Molecular Dynamics Simulations
BIOCHEMISTRY, 53:7625-7640, DEC 9 2014
abstract, full text, DOI:10.1021/bi501111j

Souza, Caio S.; Amaral, Cristiano; Treptow, Werner
Electric fingerprint of voltage sensor domains
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 111:17510-17515, DEC 9 2014
abstract, full text, DOI:10.1073/pnas.1413971111

Jayaram, B.; Dhingra, Priyanka; Mishra, Avinash; Kaushik, Rahul; Mukherjee, Goutam; Singh, Ankita; Shekhar, Shashank
Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins
BMC BIOINFORMATICS, 15 Art. No. S7, DEC 8 2014
abstract, full text, DOI:10.1186/1471-2105-15-S16-S7

Semino, Rocio; Zaldivar, Gervasio; Calvo, Ernesto J.; Laria, Daniel
Lithium solvation in dimethyl sulfoxide-acetonitrile mixtures
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 214509, DEC 7 2014
abstract, full text, DOI:10.1063/1.4902837

Starzyk, Joanna; Gruszecki, Marcin; Tutaj, Krzysztof; Luchowski, Rafal; Szlazak, Radoslaw; Wasko, Piotr; Grudzinski, Wojciech; Czub, Jacek; Gruszecki, Wieslaw I.
Self-Association of Amphotericin B: Spontaneous Formation of Molecular Structures Responsible for the Toxic Side Effects of the Antibiotic
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13821-13832, DEC 4 2014
abstract, full text, DOI:10.1021/jp510245n

Shi, Wei; Hong, Lei; Damodaran, Krishnan; Nulwala, Hunaid B.; Luebke, David R.
Molecular Simulation and Experimental Study of CO2 Absorption in Ionic Liquid Reverse Micelle
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13870-13881, DEC 4 2014
abstract, full text, DOI:10.1021/jp509282h

Sahillioglu, Ali Can; Sumbul, Fidan; Ozoren, Nesrin; Haliloglu, Turkan
Structural and Dynamics Aspects of ASC Speck Assembly
STRUCTURE, 22:1722-1734, DEC 2 2014
abstract, full text, DOI:10.1016/j.str.2014.09.011

Liu, Ming S.; Wang, Die; Morimoto, Hiroyuki; Yim, Howard C. H.; Irving, Aaron T.; Williams, Bryan R. G.; Sadler, Anthony J.
Molecular dynamics reveal a novel kinase-substrate interface that regulates protein translation
JOURNAL OF MOLECULAR CELL BIOLOGY, 6:473-485, DEC 2014
abstract, full text, DOI:10.1093/jmcb/mju044

Dorn, Marcio; Barbachan e Silva, Mariel; Buriol, Luciana S.; Lamb, Luis C.
Three-dimensional protein structure prediction: Methods and computational strategies
COMPUTATIONAL BIOLOGY AND CHEMISTRY, 53:251-276, DEC 2014
abstract, full text, DOI:10.1016/j.compbiolchem.2014.10.001

Peters, Gunther H.; Werge, Mikkel; Elf-Lind, Maria Northved; Madsen, Jesper J.; Velardez, Gustavo F.; Westh, Peter
Interaction of neurotransmitters with a phospholipid bilayer: A molecular dynamics study
CHEMISTRY AND PHYSICS OF LIPIDS, 184:7-17, DEC 2014
abstract, full text, DOI:10.1016/j.chemphyslip.2014.08.003

Schoeler, Constantin; Malinowska, Klara H.; Bernardi, Rafael C.; Milles, Lukas F.; Jobst, Markus A.; Durner, Ellis; Ott, Wolfgang; Fried, Daniel B.; Bayer, Edward A.; Schulten, Klaus; Gaub, Hermann E.; Nash, Michael A.
Ultrastable cellulosome-adhesion complex tightens under load
NATURE COMMUNICATIONS, 5 Art. No. 5635, DEC 2014
abstract, full text, TCBG publications, DOI:10.1038/ncomms6635

Kalimeri, Maria; Girard, Eric; Madern, Dominique; Sterpone, Fabio
Interface Matters: The Stiffness Route to Stability of a Thermophilic Tetrameric Malate Dehydrogenase
PLOS ONE, 9 Art. No. e113895, DEC 1 2014
abstract, full text, DOI:10.1371/journal.pone.0113895

Li, Tianxia; Yang, Dejun; Zhong, Shijun; Thomas, Joseph M.; Xue, Fengtian; Liu, Jingnan; Kong, Lingbo; Voulalas, Pamela; Hassan, Hazem E.; Park, Jae-Sung; MacKerell, Alexander D., Jr.; Smith, Wanli W.
Novel LRRK2 GTP-binding inhibitors reduced degeneration in Parkinson's disease cell and mouse models
HUMAN MOLECULAR GENETICS, 23:6212-6222, DEC 1 2014
abstract, full text, DOI:10.1093/hmg/ddu341

Mahdavi, Somayeh; Kuyucak, Serdar
Systematic Study of Binding of mu-Conotoxins to the Sodium Channel Na(V)1.4
TOXINS, 6:3454-3470, DEC 2014
abstract, full text, DOI:10.3390/toxins6123454

du Bourg, Lila Bouessel; Ortiz, Aurelie U.; Boutin, Anne; Coudert, Francois-Xavier
Thermal and mechanical stability of zeolitic imidazolate frameworks polymorphs
APL MATERIALS, 2 Art. No. 124110, DEC 2014
abstract, full text, DOI:10.1063/1.4904818

Ma, Buyong; Kolb, Stephanie; Diprima, Michael; Karna, Molleshree; Tosato, Giovanna; Yang, Qiqi; Huang, Qiang; Nussinov, Ruth
Investigation of the interactions between the EphB2 receptor and SNEW peptide variants
GROWTH FACTORS, 32:236-246, DEC 2014
abstract, full text, DOI:10.3109/08977194.2014.985786

Elward, Jennifer M.; Irudayanathan, Flaviyan Jerome; Nangia, Shikha; Chakraborty, Arindam
Optical Signature of Formation of Protein Corona in the Firefly Luciferase-CdSe Quantum Dot Complex
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:5224-5228, DEC 2014
abstract, full text, DOI:10.1021/ct500681m

Comer, Jeffrey; Phillips, James C.; Schulten, Klaus; Chipot, Christophe
Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:5276-5285, DEC 2014
abstract, full text, TCBG publications, DOI:10.1021/ct500874p

Sahu, Indra D.; Hustedt, Eric J.; Ghimire, Harishchandra; Inbaraj, Johnson J.; McCarrick, Robert M.; Lorigan, Gary A.
CW dipolar broadening EPR spectroscopy and mechanically aligned bilayers used to measure distance and relative orientation between two TOAC spin labels on an antimicrobial peptide
JOURNAL OF MAGNETIC RESONANCE, 249:72-79, DEC 2014
abstract, full text, DOI:10.1016/j.jmr.2014.09.020

Delacour, Herve; Lushchekina, Sofya; Mabboux, Isabelle; Ceppa, Franck; Masson, Patrick; Schopfer, Lawrence M.; Lockridge, Oksana
Characterization of a novel butyrylcholinesterase point mutation (p.Ala34Val), "silent" with mivacurium
BIOCHEMICAL PHARMACOLOGY, 92:476-483, DEC 1 2014
abstract, full text, DOI:10.1016/j.bcp.2014.09.014

Pietra, Francesco
Molecular Dynamics Simulation of Dioxygen Pathways through Mini Singlet Oxygen Generator (miniSOG), a Genetically Encoded Marker and Killer Protein
CHEMISTRY & BIODIVERSITY, 11:1883-1891, DEC 2014
abstract, full text, DOI:10.1002/cbdv.201400125

Jardon-Valadez, Eduardo; Bondar, Ana-Nicoleta; Tobias, Douglas J.
Electrostatic interactions and hydrogen bond dynamics in chloride pumping by halorhodopsin
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1837:1964-1972, DEC 2014
abstract, full text, DOI:10.1016/j.bbabio.2014.09.006

Woelke, Anna Lena; Galstyan, Gegham; Knapp, Ernst-Walter
Lysine 362 in cytochrome c oxidase regulates opening of the K-channel via changes in pK(A) and conformation
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, 1837:1998-2003, DEC 2014
abstract, full text, DOI:10.1016/j.bbabio.2014.08.003

Ungvarsky, Jan; Plsikova, Jana; Janovec, Ladislav; Koval, Jan; Mikes, Jaromir; Mikesova, Lucia; Harvanova, Denisa; Fedorocko, Peter; Kristian, Pavol; Kasparkova, Jana; Brabec, Viktor; Vojtickova, Maria; Sabolova, Danica; Stramova, Zuzana; Rosocha, Jan; Imrich, Jan; Kozurkova, Maria
Novel trisubstituted acridines as human telomeric quadruplex binding ligands
BIOORGANIC CHEMISTRY, 57:13-29, DEC 2014
abstract, full text, DOI:10.1016/j.bioorg.2014.07.010

Bagatin, Mariane Cristovao; Suniga Tozatti, Camila Santos; Abiko, Layara Akemi; dos Santos Yamazaki, Diego Alberto; Alves Silva, Priscila Rebeca; Perego, Leonardo Martins; Audi, Elisabeth Aparecida; Vicente Seixas, Flavio Augusto; Basso, Ernani Abicht; Gauze, Gisele de Freitas
Molecular Docking and Panicolytic Effect of 8-Prenylnaringenin in the Elevated T-Maze
CHEMICAL & PHARMACEUTICAL BULLETIN, 62:1231-1237, DEC 2014
abstract, full text

Hundt, Nikolas; Preller, Matthias; Swolski, Olga; Ang, Angella M.; Mannherz, Hans G.; Manstein, Dietmar J.; Mueller, Mirco
Molecular mechanisms of disease-related human beta-actin mutations p.R183W and p.E364K
FEBS JOURNAL, 281:5279-5291, DEC 2014
abstract, full text, DOI:10.1111/febs.13068

Kim, Soo-Kyung; Goddard, William A., I.I.I.
Predicted 3D structures of olfactory receptors with details of odorant binding to OR1G1
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 28:1175-1190, DEC 2014
abstract, full text, DOI:10.1007/s10822-014-9793-4

Virginia Saavedra-Velez, Margarita; Correa-Basurto, Jose; Matus, Myrna H.; Gasca-Perez, Eloy; Bello, Martiniano; Cuevas-Hernandez, Roberto; Virginia Garcia-Rodriguez, Rosa; Trujillo-Ferrara, Jose; Rafael Ramos-Morales, Fernando
Seeking potential anticonvulsant agents that target GABA(A) receptors using experimental and theoretical procedures
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 28:1217-1232, DEC 2014
abstract, full text, DOI:10.1007/s10822-014-9798-z

Lipovsek, Marcela; Fierro, Angelica; Perez, Edwin G.; Boffi, Juan C.; Millar, Neil S.; Fuchs, Paul A.; Katz, Eleonora; Belen Elgoyhen, Ana
Tracking the Molecular Evolution of Calcium Permeability in a Nicotinic Acetylcholine Receptor
MOLECULAR BIOLOGY AND EVOLUTION, 31:3250-3265, DEC 2014
abstract, full text, DOI:10.1093/molbev/msu258

Nakano, Shogo; Dadashipour, Mohammad; Asano, Yasuhisa
Structural and functional analysis of hydroxynitrile lyase from Baliospermum montanum with crystal structure, molecular dynamics and enzyme kinetics
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1844:2059-2067, DEC 2014
abstract, full text, DOI:10.1016/j.bbapap.2014.09.004

Strohalmova-Bohmova, Karolina; Spiwok, Vojtech; Lepsik, Martin; Hadravova, Romana; Krizova, Ivana; Ulbrich, Pavel; Pichova, Iva; Bednarova, Lucie; Ruml, Tomas; Rumlova, Michaela
Role of Mason-Pfizer Monkey Virus CA-NC Spacer Peptide-Like Domain in Assembly of Immature Particles
JOURNAL OF VIROLOGY, 88:14148-14160, DEC 2014
abstract, full text, DOI:10.1128/JVI.02286-14

Persson, Egon; Madsen, Jesper J.; Olsen, Ole H.
The length of the linker between the epidermal growth factor-like domains in factor VIIa is critical for a productive interaction with tissue factor
PROTEIN SCIENCE, 23:1717-1727, DEC 2014
abstract, full text, DOI:10.1002/pro.2553

Cui, Di; Ou, Shuching; Patel, Sandeep
Protein-Spanning Water Networks and Implications for Prediction of Protein-Protein Interactions Mediated through Hydrophobic Effects
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:3312-3326, DEC 2014
abstract, full text, DOI:10.1002/prot.24683

Li, Qing; Scholl, Zackary N.; Marszalek, Piotr E.
Capturing the Mechanical Unfolding Pathway of a Large Protein with Coiled-Coil Probes
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, 53:13429-13433, DEC 1 2014
abstract, full text, DOI:10.1002/anie.201407211

Pinto da Silva, Luis; Esteves da Silva, Joaquim C. G.
A Theoretical Analysis of the Potential Role of pi-pi Stacking Interactions in the Photoprotolytic Cycle of Firefly Luciferin
CHEMPHYSCHEM, 15:3761-3767, DEC 1 2014
abstract, full text, DOI:10.1002/cphc.201402558

Pillai, Jitesh K.; Venkadesh, Sarkarai; Ajees, A. Abdul; Rosen, Barry P.; Bhattacharjee, Hiranmoy
Mutations in the ArsA ATPase that restore interaction with the ArsD metallochaperone
BIOMETALS, 27:1263-1275, DEC 2014
abstract, full text, DOI:10.1007/s10534-014-9788-6

Grizel, Anastasia; Popinako, Anna; Kasimova, Marina A.; Stevens, Louisa; Karlova, Maria; Moisenovich, Mikhail M.; Sokolova, Olga S.
Domain Structure and Conformational Changes in rat K(V)2.1 ion Channel
JOURNAL OF NEUROIMMUNE PHARMACOLOGY, 9:727-739, DEC 2014
abstract, full text, DOI:10.1007/s11481-014-9565-x

Boynton, P.; Balatsky, A. V.; Schuller, I. K.; Di Ventra, M.
Improving sequencing by tunneling with multiplexing and cross-correlations
JOURNAL OF COMPUTATIONAL ELECTRONICS, 13:794-800, DEC 2014
abstract, full text, DOI:10.1007/s10825-014-0571-2

Belkin, Maxim; Chao, Shu-Han; Giannetti, Gino; Aksimentiev, Aleksei
Modeling thermophoretic effects in solid-state nanopores
JOURNAL OF COMPUTATIONAL ELECTRONICS, 13:826-838, DEC 2014
abstract, full text, DOI:10.1007/s10825-014-0594-8

Polak, Andraz; Tarek, Mounir; Tomsic, Matija; Valant, Janez; Ulrih, Natasa Poklar; Jamnik, Andrej; Kramar, Peter; Miklavcic, Damijan
Electroporation of archaeal lipid membranes using MD simulations
BIOELECTROCHEMISTRY, 100:18-26, DEC 2014
abstract, full text, DOI:10.1016/j.bioelechem.2013.12.006

Olavarria, K.; De Ingeniis, J.; Zielinski, D. C.; Fuentealba, M.; Munoz, R.; McCloskey, D.; Feist, A. M.; Cabrera, R.
Metabolic impact of an NADH-producing glucose-6-phosphate dehydrogenase in Escherichia coli
MICROBIOLOGY-SGM, 160:2780-2793, DEC 2014
abstract, full text, DOI:10.1099/mic.0.082180-0

Alberga, Domenico; Nicolotti, Orazio; Lattanzi, Gianluca; Nicchia, Grazia Paola; Frigeri, Antonio; Pisani, Francesco; Benfenati, Valentina; Mangiatordi, Giuseppe Felice
A new gating site in human aquaporin-4: Insights from molecular dynamics simulations
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:3052-3060, DEC 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.08.015

Vermaas, Josh V.; Tajkhorshid, Emad
Conformational heterogeneity of alpha-synuclein in membrane
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:3107-3117, DEC 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.08.012

Deleu, Magali; Crowet, Jean-Marc; Nasir, Mehmet N.; Lins, Laurence
Complementary biophysical tools to investigate lipid specificity in the interaction between bioactive molecules and the plasma membrane: A review
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:3171-3190, DEC 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.08.023

Schillinger, Anne-Sophie; Grauffel, Cedric; Khan, Hanif Muhammad; Halskau, Oyvind; Reuter, Nathalie
Two homologous neutrophil serine proteases bind to POPC vesicles with different affinities: When aromatic amino acids matter
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 1838:3191-3202, DEC 2014
abstract, full text, DOI:10.1016/j.bbamem.2014.09.003

Benavidez, Tomas E.; Torrente, Daniel; Marucho, Marcelo; Garcia, Carlos D.
Adsorption and catalytic activity of glucose oxidase accumulated on OTCE upon the application of external potential
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 435:164-170, DEC 1 2014
abstract, full text, DOI:10.1016/j.jcis.2014.08.012

Adamczyk, Zbigniew; Jamrozy, Krzysztof; Batys, Piotr; Michna, Aneta
Influence of ionic strength on poly(diallyldimethylammonium chloride) macromolecule conformations in electrolyte solutions
JOURNAL OF COLLOID AND INTERFACE SCIENCE, 435:182-190, DEC 1 2014
abstract, full text, DOI:10.1016/j.jcis.2014.07.037

Abdul-Ridha, Alaa; Lane, J. Robert; Mistry, Shailesh N.; Lopez, Laura; Sexton, Patrick M.; Scammells, Peter J.; Christopoulos, Arthur; Canals, Meritxell
Mechanistic Insights into Allosteric Structure-Function Relationships at the M-1 Muscarinic Acetylcholine Receptor
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:33701-33711, NOV 28 2014
abstract, full text, DOI:10.1074/jbc.M114.604967

Chatterjee, Prathit; Bagchi, Sayan; Sengupta, Neelanjana
The non-uniform early structural response of globular proteins to cold denaturing conditions: A case study with Yfh1
JOURNAL OF CHEMICAL PHYSICS, 141 Art. No. 205103, NOV 28 2014
abstract, full text, DOI:10.1063/1.4901897

Budnjo, Adnan; Narawane, Shailesh; Grauffel, Cedric; Schillinger, Anne-Sophie; Fossen, Torgils; Reuter, Nathalie; Haug, Bengt Erik
Reversible Ketomethylene-Based Inhibitors of Human Neutrophil Proteinase 3
JOURNAL OF MEDICINAL CHEMISTRY, 57:9396-9408, NOV 27 2014
abstract, full text, DOI:10.1021/jm500782s

Khrenova, Maria G.; Savitsky, Alexander P.; Topol, Igor A.; Nemukhin, Alexander V.
Exploration of the Zinc Finger Motif in Controlling Activity of Matrix Metalloproteinases
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13505-13512, NOV 27 2014
abstract, full text, DOI:10.1021/jp5088702

Baker, Michelle K.; Abrams, Cameron F.
Dynamics of Lipids, Cholesterol, and Transmembrane alpha-Helices from Microsecond Molecular Dynamics Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13590-13600, NOV 27 2014
abstract, full text, DOI:10.1021/jp507027t

James, Kevin A.; Verkhivker, Gennady M.
Structure-Based Network Analysis of Activation Mechanisms in the ErbB Family of Receptor Tyrosine Kinases: The Regulatory Spine Residues Are Global Mediators of Structural Stability and Allosteric Interactions
PLOS ONE, 9 Art. No. e113488, NOV 26 2014
abstract, full text, DOI:10.1371/journal.pone.0113488

Laine, Jennifer M.; Amat, Miguel; Morgan, Brittany R.; Royer, William E., Jr.; Massi, Francesca
Insight into the Allosteric Mechanism of Scapharca Dimeric Hemoglobin
BIOCHEMISTRY, 53:7199-7210, NOV 25 2014
abstract, full text, DOI:10.1021/bi500591s

Bera, Manindra; Kotamarthi, Hema Chandra; Dutta, Subarna; Ray, Angana; Ghosh, Saptaparni; Bhattacharyya, Dhananjay; Ainavarapu, Sri Rama Koti; Sengupta, Kaushik
Characterization of Unfolding Mechanism of Human Lamin A Ig Fold by Single-Molecule Force Spectroscopy-Implications in EDMD
BIOCHEMISTRY, 53:7247-7258, NOV 25 2014
abstract, full text, DOI:10.1021/bi500726f

Lim, San Sui; Yang, Wei; Krishnarjuna, Bankala; Sivaraman, Komagal Kannan; Chandrashekaran, Indu R.; Kass, Itamar; MacRaild, Christopher A.; Devine, Shane M.; Debono, Cael O.; Anders, Robin F.; Scanlon, Martin J.; Scammells, Peter J.; Norton, Raymond S.; McGowan, Sheena
Structure and Dynamics of Apical Membrane Antigen 1 from Plasmodium falciparum FVO
BIOCHEMISTRY, 53:7310-7320, NOV 25 2014
abstract, full text, DOI:10.1021/bi5012089

Zhang, Li; Liu, Zhipei; Ren, Tao; Wu, Pan; Shen, Jia-Wei; Zhang, Wei; Wang, Xinping
Understanding the Structure of Hydrophobic Surfactants at the Air/Water Interface from Molecular Level
LANGMUIR, 30:13815-13822, NOV 25 2014
abstract, full text, DOI:10.1021/la5030586

Yang, J.; Singharoy, A.; Sereda, Yu. V.; Ortoleva, P. J.
Quasiequivalence of multiscale coevolution and ensemble MD simulations: A demonstration with lactoferrin
CHEMICAL PHYSICS LETTERS, 616:154-160, NOV 25 2014
abstract, full text, DOI:10.1016/j.cplett.2014.10.020

Shang, Zhiguo; Zhou, Kaifeng; Xu, Chen; Csencsits, Roseann; Cochran, Jared C.; Sindelar, Charles V.
High-resolution structures of kinesin on microtubules provide a basis for nucleotide-gated force generation
ELIFE, 3 Art. No. e04686, NOV 21 2014
abstract, full text, DOI:10.7554/eLife.04686

Perlinska, Agata; Grynberg, Marcin
Bacillus anthracis pXO1 plasmid encodes a putative membrane-bound bacteriocin
PEERJ, 2 Art. No. UNSP e679, NOV 20 2014
abstract, full text, DOI:10.7717/peerj.679

Furini, Simone; Domene, Carmen
DNA Recognition Process of the Lactose Repressor Protein Studied via Metadynamics and Umbrella Sampling Simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 118:13059-13065, NOV 20 2014
abstract, full text, DOI:10.1021/jp505885j

Aranda, Juan; Zinovjev, Kirill; Roca, Maite; Tunon, Inaki
Dynamics and Reactivity in Thermus aquaticus N6-Adenine Methyltransferase
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:16227-16239, NOV 19 2014
abstract, full text, DOI:10.1021/ja5077124

Kastner, Kevin W.; Shoue, Douglas A.; Estiu, Guillermina L.; Wolford, Julia; Fuerst, Megan F.; Markley, Lowell D.; Izaguirre, Jesus A.; McDowell, Mary Ann
Characterization of the Anopheles gambiae octopamine receptor and discovery of potential agonists and antagonists using a combined computational-experimental approach
MALARIA JOURNAL, 13 Art. No. 434, NOV 18 2014
abstract, full text, DOI:10.1186/1475-2875-13-434

Carson, Spencer; Wilson, James; Aksimentiev, Aleksei; Wanunu, Meni
Smooth DNA Transport through a Narrowed Pore Geometry
BIOPHYSICAL JOURNAL, 107:2381-2393, NOV 18 2014
abstract, full text, DOI:10.1016/j.bpj.2014.10.017

Sayer, James R.; Wallden, Karin; Pesnot, Thomas; Campbell, Frederick; Gane, Paul J.; Simone, Michela; Koss, Hans; Buelens, Floris; Boyle, Timothy P.; Selwood, David L.; Waksman, Gabriel; Tabor, Alethea B.
2-and 3-substituted imidazo[1,2-a]pyrazines as inhibitors of bacterial type IV secretion
BIOORGANIC & MEDICINAL CHEMISTRY, 22:6459-6470, NOV 15 2014
abstract, full text, DOI:10.1016/j.bmc.2014.09.036

Padhi, Siladitya; Burri, Raghunadha Reddy; Jameel, Shahid; Priyakumar, U. Deva
Atomistic Detailed Mechanism and Weak Cation-Conducting Activity of HIV-1 Vpu Revealed by Free Energy Calculations
PLOS ONE, 9 Art. No. e112983, NOV 13 2014
abstract, full text, DOI:10.1371/journal.pone.0112983

Wei, Chenyu; Pohorille, Andrew
Flip-Flop of Oleic Acid in a Phospholipid Membrane: Rate and Mechanism
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12919-12926, NOV 13 2014
abstract, full text, DOI:10.1021/jp508163e

Perez-Aguilar, Jose Manuel; Shan, Jufang; LeVine, Michael V.; Khelashvili, George; Weinstein, Harel
A Functional Selectivity Mechanism at the Serotonin-2A GPCR Involves Ligand-Dependent Conformations of Intracellular Loop 2
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 136:16044-16054, NOV 12 2014
abstract, full text, DOI:10.1021/ja508394x

Asthana, Shailendra; Shukla, Saumya; Ruggerone, Paolo; Vargiu, Attilio V.
Molecular Mechanism of Viral Resistance to a Potent Non-nucleoside Inhibitor Unveiled by Molecular Simulations
BIOCHEMISTRY, 53:6941-6953, NOV 11 2014
abstract, full text, DOI:10.1021/bi500490z

Andreasen, Maria; Skeby, Katrine Kirkeby; Zhang, Shuai; Nielsen, Erik Holm; Klausen, Lasse Hyldgaard; Frahm, Heidi; Christiansen, Gunna; Skrydstrup, Troels; Dong, Mingdong; Schiott, Birgit; Otzen, Daniel
The Importance of Being Capped: Terminal Capping of an Amyloidogenic Peptide Affects Fibrillation Propensity and Fibril Morphology
BIOCHEMISTRY, 53:6968-6980, NOV 11 2014
abstract, full text, DOI:10.1021/bi500674u

Krishnan, Subramanian; Liu, Fan; Abrol, Ravinder; Hodges, Jacqueline; Goddard, William A., I.I.I.; Prasadarao, Nemani V.
The Interaction of N-Glycans in Fc gamma Receptor I alpha-Chain with Escherichia coli K1 Outer Membrane Protein A for Entry into Macrophages EXPERIMENTAL AND COMPUTATIONAL ANALYSIS
JOURNAL OF BIOLOGICAL CHEMISTRY, 289:30937-30949, NOV 7 2014
abstract, full text, DOI:10.1074/jbc.M114.599407

Panecka, Joanna; Mura, Cameron; Trylska, Joanna
Interplay of the Bacterial Ribosomal A-Site, S12 Protein Mutations and Paromomycin Binding: A Molecular Dynamics Study
PLOS ONE, 9 Art. No. e111811, NOV 7 2014
abstract, full text, DOI:10.1371/journal.pone.0111811

Sathe, Chaitanya; Girdhar, Anuj; Leburton, Jean-Pierre; Schulten, Klaus
Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores
NANOTECHNOLOGY, 25 Art. No. 445105, NOV 7 2014
abstract, full text, TCBG publications, DOI:10.1088/0957-4484/25/44/445105

Dong, Hao; Fiorin, Giacomo; DeGrado, William F.; Klein, Michael L.
Proton Release from the Histidine-Tetrad in the M2 Channel of the Influenza A Virus
JOURNAL OF PHYSICAL CHEMISTRY B, 118:12644-12651, NOV 6 2014
abstract, full text, DOI:10.1021/jp5102225

Craddock, Travis John Adrian; Friesen, Douglas; Mane, Jonathan; Hameroff, Stuart; Tuszynski, Jack A.
The feasibility of coherent energy transfer in microtubules
JOURNAL OF THE ROYAL SOCIETY INTERFACE, 11 Art. No. UNSP 20140677, NOV 6 2014
abstract, full text, DOI:10.1098/rsif.2014.0677

Chen, Rong; Gryn'ova, Ganna; Wu, Yingliang; Coote, Michelle L.; Chung, Shin-Ho
Mechanisms and Energetics of Potassium Channel Block by Local Anesthetics and Antifungal Agents
BIOCHEMISTRY, 53:6786-6792, NOV 4 2014
abstract, full text, DOI:10.1021/bi5009408

Petukh, Marharyta; Wu, Bohua; Stefl, Shannon; Smith, Nick; Hyde-Volpe, David; Wang, Li; Alexov, Emil
Chronic Beryllium Disease: Revealing the Role of Beryllium Ion and Small Peptides Binding to HLA-DP2
PLOS ONE, 9 Art. No. e111604, NOV 4 2014
abstract, full text, DOI:10.1371/journal.pone.0111604

Arcario, Mark J.; Tajkhorshid, Emad
Membrane-Induced Structural Rearrangement and Identification of a Novel Membrane Anchor in Talin F2F3
BIOPHYSICAL JOURNAL, 107:2059-2069, NOV 4 2014
abstract, full text, DOI:10.1016/j.bpj.2014.09.022

Blanchard, Andrew E.; Arcario, Mark J.; Schulten, Klaus; Tajkhorshid, Emad
A Highly Tilted Membrane Configuration for the Prefusion State of Synaptobrevin
BIOPHYSICAL JOURNAL, 107:2112-2121, NOV 4 2014
abstract, full text, TCBG publications, DOI:10.1016/j.bpj.2014.09.013

Woelke, Anna Lena; Wagner, Anke; Galstyan, Gegham; Meyer, Tim; Knapp, Ernst-Walter
Proton Transfer in the K-Channel Analog of B-Type Cytochrome c Oxidase from Thermus thermophilus
BIOPHYSICAL JOURNAL, 107:2177-2184, NOV 4 2014
abstract, full text, DOI:10.1016/j.bpj.2014.09.010

Anwar-Mohamed, Anwar; Barakat, Khaled H.; Bhat, Rakesh; Noskov, Sergei Y.; Tyrrell, D. Lorne; Tuszynski, Jack A.; Houghton, Michael
A human ether-a-go-go-related (hERG) ion channel atomistic model generated by long supercomputer molecular dynamics simulations and its use in predicting drug cardiotoxicity
TOXICOLOGY LETTERS, 230:382-392, NOV 4 2014
abstract, full text, DOI:10.1016/j.toxlet.2014.08.007

Stewart, Matthew B.; Gray, Stephen R.; Vasiljevic, Todor; Orbell, John D.
The role of poly-M and poly-GM sequences in the metal-mediated assembly of alginate gels
CARBOHYDRATE POLYMERS, 112:486-493, NOV 4 2014
abstract, full text, DOI:10.1016/j.carbpol.2014.06.001

Klose, Daniel; Voskoboynikova, Natalia; Orban-Glass, Ioan; Rickert, Christian; Engelhard, Martin; Klare, Johann P.; Steinhoff, Heinz-Juergen
Light-induced switching of HAMP domain conformation and dynamics revealed by time-resolved EPR spectroscopy
FEBS LETTERS, 588:3970-3976, NOV 3 2014
abstract, full text, DOI:10.1016/j.febslet.2014.09.012

Neuhaeuser, Benjamin; Dynowski, Marek; Ludewig, Uwe
Switching substrate specificity of AMT/MEP/Rh proteins
CHANNELS, 8:496-502, NOV-DEC 2014
abstract, full text, DOI:10.4161/19336950.2014.967618

Carvalho, Alexandra T. P.; Barrozo, Alexandre; Doron, Dvir; Kilshtain, Alexandra Vardi; Major, Dan Thomas; Kamerlin, Shina Caroline Lynn
Challenges in computational studies of enzyme structure, function and dynamics
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 54:62-79, NOV 2014
abstract,