We are proud to announce our 63rd Hands-on Workshop on Computational Biophysics this summer.

Dates: August 4 - 8, 2025
Location: Leach Science Center, Auburn University
Application Deadline: June 20, 2025

The workshop is ideal for students and researchers from computational and biophysical backgrounds; non-specialists eager to learn computational biophysics methods are also welcome to apply. Topics include molecular dynamics simulations using NAMD 3.0, biomolecular visualization and analysis using VMD 2.0, and advanced modeling, simulation, and analysis methods utilizing NAMD and VMD Plug-Ins.

Click here for more information and to apply.

Cholesterol, an important fat molecule, regulates the structure and function of many membrane proteins. Computational studies of protein-cholesterol interactions have been long impeded by the slow dynamics of lipids like cholesterol. In a recent paper, Resource researchers report a new generation of an accelerated membrane model (HMMM) in which cholesterol can be included. Utilizing NAMD and in-house Tcl scripts with VMD, the new model successfully identifies cholesterol binding sites on proteins and captures detailed lipid interactions in agreement with experimental data.

Glutamate transporters maintain brain health by clearing the main excitatory neurotransmitter, glutamate, from synapses. Their dysfunction is linked to neurological conditions such as Alzheimer and Parkinson. In a recent publication in PNAS, Resource researchers characterized the most detailed view of operation of a bacterial glutamate transporters using advanced molecular dynamics simulations with NAMD. The study revealed a sophisticated "elevator-like" mechanism involving both translational and rotational shifts within the protein. Researchers also demonstrated how surrounding lipids influence transporter function. The results enhance our understanding of neurotransmitter regulation, aiding in the design of new therapies for neurological disorders.

As a part of the 2025 Beckman Institute Open House (BIOH), the Theoretical and Computational Biophysics Group (TCBG) offered an exciting and immersive glimpse into the molecular world of modern biology through cutting-edge virtual reality (VR) experiences. As developers of the widely used molecular simulation tools NAMD and VMD, TCBG takes pride in making science accessible to and inspiring for the broader community. At this year's BIOH, visitors had the opportunity to fly through molecular structures, manipulate DNA interactively, and step inside protein complexes that power living cells, all in VR. A standout attraction was the Minecraft-style virtual cell exploration, where guests navigated through blocky but biologically accurate cellular environments generated from real 3D microscopy data. The event drew curious minds of all ages, from young aspiring students to seasoned researchers, showcasing TCBG's ongoing mission to bridge science, technology, and public engagement.

VMD 2.0 is here! This early alpha release marks a significant upgrade to the widely used molecular visualization and analysis software, introducing a streamlined interface, improved selection tools, and cutting-edge performance enhancements. Further development is ongoing, with new features continuously added. Learn more and follow the progress here: VMD 2.0 Introduction.

Major feature enhancements in VMD 2.0 include:

• A redesigned user interface providing a more intuitive and efficient experience; new action buttons provide quick access to basic functions, while an improved selection engine allows for precise molecular filtering.

• Fast & scalable secondary structure calculation

• High-performance glycan visualization

• Rapid & efficient surface calculation

• Real-time interactive ray tracing

With these enhancements and more on the way, VMD 2.0 is shaping the future of molecular visualization. Stay updated and try the latest release: VMD 2.0 Introduction.

Staphylococcus aureus, a prominent human pathogen, employs a specific enzyme to evade the immune system. This enzyme converts antimicrobial fatty acids in the cellular membrane into anti-inflammatory compounds that protect the pathogen against the host inflammatory response. Understanding the membrane-binding mechanism of this enzyme is essential for developing new strategies to combat S. aureus infections.

As highlighted in our recent publication in J. Biol. Chem., Resource researchers employed molecular dynamics simulations using NAMD to study this mechanism. Utilizing a specifically designed membrane model with enhanced lipid motion, they captured how the enzyme binds to the membrane and described its pose within the membrane. These findings provide molecular insights into S. aureus' virulence and highlight potential targets for novel therapeutic interventions.

Nearly 80% of the patients suffering from glycogen storage disease have a single mutation in their genome. The product of this gene mediates critical steps in sugar metabolism and storage. However, the molecular basis for the malfunction caused by this and similar mutations has remained unknown due to a lack of structural data. The advent of AlphaFold provided us with the first model of this important protein. As reported in a recent publication in PNAS Nexus, Resource researchers have produced large conformational ensembles of this protein in the empty and sugar-bound forms for both native and 10 clinically-relevant mutants. By identifying the structural and energetic effects of such mutations, using NAMD and VMD, we have begun to elucidate the role of each residue in the dysfunction of the enzyme.