James C. Gumbart

Publication Activity (10 Years)

Years Active: 2005-2020
Publications (10 Years): 5

Top Topics

Molecular Dynamics Simulations

Amino Acid Sequences

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

PLoS Comput. Biol.

Comput. Phys. Commun.

Publications

Atanu Acharya, Rupesh Agarwal, Matthew B. Baker, Jérôme Baudry, Debsindhu Bhowmik, Swen Böhm, Kendall G. Byler, Sam Yen-Chi Chen, Leighton Coates, Connor J. Cooper, Omar Demerdash, Isabella Daidone, John D. Eblen, Sally R. Ellingson, Stefano Forli, Jens Glaser, James C. Gumbart, John Gunnels, Oscar R. Hernandez, Stephan Irle, D. W. Kneller, A. Kovalevsky, Jeffrey M. Larkin, Travis J. Lawrence, Scott LeGrand, Shih-Hsien Liu, Julie C. Mitchell, Gilchan Park, Jerry M. Parks, Anna Pavlova, Loukas Petridis, Duncan Poole, Line Pouchard, Arvind Ramanathan, David M. Rogers, Diogo Santos-Martins, Aaron Scheinberg, Ada Sedova, Y. Shen, Jeremy C. Smith, Micholas Dean Smith, Carlos Soto, Aristides Tsaris, Mathialakan Thavappiragasam, Andreas F. Tillack, Josh Vincent Vermaas, Van Quan Vuong, Junqi Yin, Shinjae Yoo, Mai Zahran, Laura Zanetti Polzi
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J. Chem. Inf. Model. 60 (12) (2020)
Hyea Hwang, Anthony Hazel, Peng Lian, Jeremy C. Smith, James C. Gumbart, Jerry M. Parks
A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins. J. Comput. Chem. 41 (6) (2020)
Jinchan Liu, James C. Gumbart
Membrane thinning and lateral gating are consistent features of BamA across multiple species. PLoS Comput. Biol. 16 (10) (2020)
Haohao Fu, James C. Gumbart, Haochuan Chen, Xueguang Shao, Wensheng Cai, Christophe Chipot
BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations. J. Chem. Inf. Model. 58 (3) (2018)
Christopher T. Lee, Jeffrey Comer, Conner Herndon, Nelson Leung, Anna Pavlova, Robert V. Swift, Chris Tung, Christopher N. Rowley, Rommie E. Amaro, Christophe Chipot, Yi Wang, James C. Gumbart
Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. J. Chem. Inf. Model. 56 (4) (2016)
Anna Pavlova, James C. Gumbart
Parametrization of macrolide antibiotics using the force field toolkit. J. Comput. Chem. 36 (27) (2015)
James C. Gumbart, Morgan Beeby, Grant J. Jensen, Benoît Roux
Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations. PLoS Comput. Biol. 10 (2) (2014)
Wei Jiang, James C. Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James C. Gumbart, Yun Luo, Klaus Schulten, Benoît Roux
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. Comput. Phys. Commun. 185 (3) (2014)
Christopher G. Mayne, Jan Saam, Klaus Schulten, Emad Tajkhorshid, James C. Gumbart
Rapid parameterization of small molecules using the force field toolkit. J. Comput. Chem. 34 (32) (2013)
Fatemeh Khalili-Araghi, Brigitte Ziervogel, Benoît Roux, James C. Gumbart
Membrane protein simulations under asymmetric ionic concentrations. XSEDE (2012)
James C. Phillips, Rosemary Braun, Wei Wang, James C. Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant V. Kalé, Klaus Schulten
Scalable molecular dynamics with NAMD. J. Comput. Chem. 26 (16) (2005)