Z. Zhao and E. Tajkhorshid (2024) GOLEM: Automated and Robust Cryo-EM-Guided Ligand Docking with Explicit Water Molecules. J. Chem. Inf. Model.

Y. Zeng, A. Pavlova, P. M. Nelson, Z. L. Glick, L. Yang, Y. T. Pang, M. Spivak, G. Licari, E. Tajkhorshid, C. D. Sherrill, and J. C. Gumbart (2024) Broadening access to small-molecule parameterization with the force field toolkit. J. Chem. Phys., 160:242501.

A. S. Arango, H. Park, and E. Tajkhorshid (2024) Topological Learning Approach to Characterizing Biological Membranes. J. Chem. Inf. Model., 64:5242-5252.

H. Park, P. Patel, R. Haas, and E. A. Huerta (2024) APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics. PNAS, 121:e2311888121.

M. Lihan and E. Tajkhorshid (2024) Improved Highly Mobile Membrane Mimetic Model for Investigating Protein–Cholesterol Interactions. J. Chem. Inf. Model., 64:4822-4834.

K. A. Munoz, R. J. Ulrich, A. K. Vasan, M. Sinclair, P. C. Wen, J. R. Holmes, H. Y. Lee, C. C. Hung, C. J. Fields, E. Tajkhorshid, G. W. Lau, and P. J. Hergenrother (2024) A Gram-negative-selective antibiotic that spares the gut microbiome. Nature, 630:429-436.

F. C. Kalutantirige, J. He, L. Yao, S. Cotty, S. Zhou, J. W. Smith, E. Tajkhorshid, C. M. Schroeder, J. S. Moore, H. An, X. Su, and Y. Li (2024) Beyond nothingness in the formation and functional relevance of voids in polymer films. Nat. Commun., 15:2852.

D. D. Dhavale, A. M. Barclay, C. G. Borcik, K. Basore, D. A. Berthold, I. R. Gordon, J. Liu, M. H. Milchberg, J. Y. O'Shea, M. J. Rau, Z. Smith, S. Sen, B. Summers, J. Smith, O. A. Warmuth, R. J. Perrin, J. S. Perlmutter, Q. Chen, J. A. J. Fitzpatrick, C. D. Schwieters, E. Tajkhorshid, C. M. RIenstra, and P. T. Kotzbauer (2024) Structure of alpha-synuclein fibrils derived from human Lewy body dementia tissue. Nat. Commun., 15:2750.

E. J. Shinn and E. Tajkhorshid (2024) Generating Concentration Gradients Across Membranes for Molecular Dynamics Simulations of Periodic Systems. Int. J. Mol. Sci., 25:3616.

B. Vallat, B. M. Webb, J. D. Westbrook, T. D. Goddard, C. A. Hanke, A. Graziadei, E. Peisach, A. Zalevsky, J. Sagendorf, H. Tangmunarunkit, S. Voinea, M. Sekharan, J. Yu, A. A. M. J. J. Bonvin, F. DiMaio, G. Hummer, J. Meiler, E. Tajkhorshid, T. E. Ferrin, C. L. Lawson, A. Leitner, J. Rappsilber, C. A. M. Seidel, C. M. Jeffries, S. K. Burley, J. C. Hoch, G. Kurisu, K. Morris, A. Patwardhan, S. Velankar, T. Schwede, J. Trewhella, C. Kesselman, H. M. Berman, and A. Sali (2024) IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. J. Mol. Biol., 18:168546.

P. Roy, J. Maturano, H. Hasdemir, A. Lopez, F. Xu, J. Hellman, E. Tajkhorshid, D. Sarlah, and A. Das (2024) Elucidating the Mechanism of Metabolism of Cannabichromene by Human Cytochrome P450s. J. Nat. Prod.

J. Zhang, Y. Yu, X. Zou, Y. Du, Q. Liang, M. Gong, Y. He, J. Luo, D. Wu, X. Jiang, M. Sinclair, E. Tajkhorshid, H. Z. Chen, Z. Hou, Y. Zheng, L. F. Chen, and X. D. Yang (2024) WSB1/2 target chromatin-bound lysine-methylated RelA for proteasomal degradation and NF-κB termination. Nucleic Acids Res., gkae161.

T. Gose, A. Rasouli, S. Dehghani-Ghahnaviyeh, P. C. Wen, Y. Wang, J. Lynch, Y. Fukuda, T. Shafi, R. C. Ford, E. Tajkhorshid, and J. D. Schultz (2024) Tumor-acquired somatic mutation affects conformation to abolish ABCG2-mediated drug resistance. Drug Resist. Updat., 73:101066.

M. Sinclair, R. A. Stein, J. H. Sheehan, E. M. Hawes, R. M. O'Brien, E. Tajkhorshid, and D. P. Claxton (2024) Integrative analysis of pathogenic variants in glucose-6-phosphatase based on an AlphaFold2 model. PNAS Nexus, 3:pgae035.

H. Park, X. Yan, R. Zhu, E. A. Huerta, S. Chaudhuri, D. Cooper, I. Foster, and E. Tajkhorshid (2024) A generative artificial intelligence framework based on a molecular diffusion model for the design of metal-organic frameworks for carbon capture. Commun. Chem., 7:21.

C. D. Radka, C. R. Grace, H. S. Hasdemir, Y. Li, C. C. Rodriguez, P. Rodrigues, M. L. Oldham, M. Z. Qayyum, A. Pitre, W. J. MacCain, R. C. Kalathur, E. Tajkhorshid, and O. Rock (2024) The carboxy terminus causes interfacial assembly of oleate hydratase on a membrane bilayer. J. Biol. Chem., 105627.

Q. Tang, M. Sinclair, H. S. Hasdemir, R. A. Stein, E. Karakas, E. Tajkhorshid, and H. S. Mchaourab (2023) Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter. Nat. Commun., 14:7184.

Y. Zhang, O. Scubas, S. Pant, F. Heinrich, A. Vogel, J. Li, Y. Li, L. A. Clifton, S. Dam, K. Bacia, D. Huster, P. A. Randazzo, M. Losche, E. Tajkhorshid, and R. A. Byrd (2023) Myr-Arf1 conformational flexibility at the membrane surface sheds light on the interactions with ArfGAP ASAP1. Nat. Commun., 14:7570.

D. Yang, Z, Zhao, E. Tajkhorshid, and E. Gouaux (2023) Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants. Proc. Natl. Acad. Sci. USA.

G. D. Galles, D. T. Infield, C. J. Clark, M. L. Hemshorn, S. Manikandan, F. Fazan, A. Rasouli, E. Tajkhorshid, J. D. Galpin, R. B. Cooley, R. A. Mehl, and C. A. Ahern (2023) Tuning phenylalanine fluorination to assess aromatic contributions to protein function and stability in cells. Nat. Commun., 14:59.

A. Rasouli, Q. Yu, S. Dehghani-Ghahnaviyeh, and E. Tajkhorshid (2022) Differential dynamics and direct interaction of bound ligands with lipids in multidrug transporter ABCG2. Proc. Natl. Acad. Sci. USA, 120:e2213437120.

L. T. My Le, J. R. Thompson, S. Dehghani-Ghahnaviyeh, S. Pant, P. X. Dang, T. Kanikeyo, E. Tajkhorshid, and A. Alam (2022) Cryo-EM structures of human ABCA7 provide insights into its phospholipid translocation mechanisms. EMBO Journal, 42:e111065.

L. Leisle, K. Lam, S. Dehghani-Ghahnaviyeh, E. Fortea, J. Galpin, C. A. Ahern, E. Tajkhorshid, and A. Accardi (2022) Backbone amides are key determinants of Cl- selectivity in CLC ion channels. Nat. Commun., 13:7508.

S. Dehghani-Ghahnaviyeh, Z. Zhao, and E. Tajkhorshid (2022) Lipid-mediated prestin organization in outer hair cell membranes and its implications in sound amplification. Nat. Commun., 13:6877.

H. Jeong, S. Clark, A. Goehring, S. Dehghani-Ghahnaviyeh, A. Rasouli, E. Tajkhorshid, and E. Gouaux (2022) Structures of the TMC-1 complex illuminate mechanosensory transduction. Nature, 610:796-803.

I. Singaram, A. Sharma, S. Pant, M. Lihan, M. J. Park, P. Buwaneka, Y. Hu, N. Mahmud, Y. M. Kim, V. Gevorgyan, I. Khan, E. Tajkhorshid, and W. Cho (2022) Targeting lipid-protein interaction for drug development: Development of a novel resistance-proof Syk inhibitor for acute myeloid leukemia. Nat. Chem. Biol.

R. Dastvan, A. Rasouli, S. Dehghani-Ghahnaviyeh, S. Gies, and E. Tajkhorshid (2022) Proton-driven alternating access in a spinster transporter, an emerging family of broad-specificity effux pumps. Nat. Commun., 13:5161.

K. Kapoor, T. Chen, and E. Tajkhorshid (2022) Post-translational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors. Proc. Natl. Acad. Sci. USA, 119:e2119761119.

A. K. Vasan, N. Haloi, R. J. Ulrich, M. E. Metcalf, P. C. Wen, W. W. Metcalf, P. J. Hergenrother, D. Shukla, and E. Tajkhorshid (2022) Role of internal loop dynamics in antibiotic permeability of outer membrane porins. Proc. Natl. Acad. Sci. USA, 119:e2117009119.