James C. Gumbart

12 papers Journal 11Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Machine Learning of Molecular Dynamics Simulations Provides Insights into the Modulation of Viral Capsid Assembly.
J. Chem. Inf. Model.
Anna Pavlova, Zixing Fan, Diane L. Lynch, James C. Gumbart
2024 J jnl
Protein Structure Prediction in the 3D HP Model Using Deep Reinforcement Learning.
CoRR
Giovanny Espitia, Yui Tik Pang, James C. Gumbart
2020 J jnl
A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins.
J. Comput. Chem.
Hyea Hwang, Anthony Hazel, Peng Lian, Jeremy C. Smith, James C. Gumbart, Jerry M. Parks
2020 J jnl
Membrane thinning and lateral gating are consistent features of BamA across multiple species.
PLoS Comput. Biol.
Jinchan Liu, James C. Gumbart
2020 J jnl
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.
J. Chem. Inf. Model.
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, Daniel W. Kneller, Andrey 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, Yue 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
2018 J jnl
BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations.
J. Chem. Inf. Model.
Haohao Fu, James C. Gumbart, Haochuan Chen, Xueguang Shao, Wensheng Cai, Christophe Chipot
2016 J jnl
Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds.
J. Chem. Inf. Model.
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
2015 J jnl
Parametrization of macrolide antibiotics using the force field toolkit.
J. Comput. Chem.
Anna Pavlova, James C. Gumbart
2014 J jnl
Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD.
Comput. Phys. Commun.
Wei Jiang, James C. Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James C. Gumbart, Yun Luo, Klaus Schulten, Benoît Roux
2013 J jnl
Rapid parameterization of small molecules using the force field toolkit.
J. Comput. Chem.
Christopher G. Mayne, Jan Saam, Klaus Schulten, Emad Tajkhorshid, James C. Gumbart
2012 — conf
Membrane protein simulations under asymmetric ionic concentrations.
XSEDE
Fatemeh Khalili-Araghi, Brigitte Ziervogel, Benoît Roux, James C. Gumbart
2005 J jnl
Scalable molecular dynamics with NAMD.
J. Comput. Chem.
James C. Phillips, Rosemary Braun, Wei Wang, James C. Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant V. Kalé, Klaus Schulten