Gumbart, James C.

Scalable molecular dynamics with NAMD

Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005) · Journal of Computational Chemistry

Protein Structure and DynamicsParallel Computing and Optimization Techniques

Cited by 16,914

Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

Gumbart, J. C., Roux, B., & Chipot, C. (2013) · Journal of Chemical Theory and Computation

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 343

Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.

Frauenfeld, J., Gumbart, J., Sluis, E. O. V. D., Funes, S., Gartmann, M., Beatrix, B., Mielke, T., Berninghausen, O., Becker, T., Schulten, K., et al. (2011) · Nature Structural & Molecular Biology

RNA and protein synthesis mechanismsAdvanced Electron Microscopy Techniques and Applications

Cited by 298

Structural basis for iron piracy by pathogenic Neisseria

Noinaj, N., Easley, N. C., Oke, M., Mizuno, N., Gumbart, J., Boura, E., Steere, A. N., Zak, O., Aisen, P., Tajkhorshid, E., et al. (2012) · Nature

Bacterial Infections and VaccinesBacterial Genetics and Biotechnology

Cited by 262

Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles

Gumbart, J. C., Roux, B., & Chipot, C. (2013) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 211

Comprehensive structure and functional adaptations of the yeast nuclear pore complex

Akey, C. W., Singh, D., Ouch, C., Echeverria, I., Nudelman, I., Varberg, J. M., Yu, Z., Fang, F., Shi, Y., Wang, J., et al. (2022) · Cell

Nuclear Structure and FunctionProtein Structure and Dynamics

Cited by 180

Structure of the SecY channel during initiation of protein translocation

Park, E., Ménétret, J.-F., Gumbart, J. C., Ludtke, S. J., Li, W., Whynot, A., Rapoport, T. A., & Akey, C. W. (2014) · Nature

RNA and protein synthesis mechanismsBacterial Genetics and Biotechnology

Cited by 148

Conformational changes of the clamp of the protein translocation ATPase SecA

Chen, Y., Bauer, B. W., Rapoport, T. A., & Gumbart, J. C. (2015) · Journal of Molecular Biology

Bacterial Genetics and BiotechnologyProtein Structure and Dynamics

Cited by 27

A Rigorous Framework for Calculating Protein–Protein Binding Affinities in Membranes

Blazhynska, M., Gumbart, J. C., Chen, H., Tajkhorshid, E., Roux, B., & Chipot, C. (2023) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsLipid Membrane Structure and Behavior

Cited by 22

DeepPath: overcoming data scarcity for protein transition pathway prediction using physics-based deep learning

Pang, Y. T., Yang, L., Kuo, K. M., & Gumbart, J. C. (2026) · Chemical Science

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 13