Scalable molecular dynamics with NAMD. - James C. Phillips; Rosemary Braun; Wei Wang 342; James C. Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D. Skeel; Laxmikant V. Kalé; Klaus Schulten (J. Comput. Chem., 2005)

Membrane protein simulations under asymmetric ionic concentrations. - Fatemeh Khalili-Araghi; Brigitte Ziervogel; Benoît Roux; James C. Gumbart (XSEDE, 2012)

Rapid parameterization of small molecules using the force field toolkit. - Christopher G. Mayne; Jan Saam; Klaus Schulten; Emad Tajkhorshid; James C. Gumbart (J. Comput. Chem., 2013)

Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. - Wei Jiang; James C. Phillips; Lei Huang 019; Mikolai Fajer; Yilin Meng; James C. Gumbart; Yun Luo; Klaus Schulten; Benoît Roux (Comput. Phys. Commun., 2014)

Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations. - James C. Gumbart; Morgan Beeby; Grant J. Jensen; Benoît Roux (PLoS Comput. Biol., 2014)

Parametrization of macrolide antibiotics using the force field toolkit. - Anna Pavlova; James C. Gumbart (J. Comput. Chem., 2015)

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds. - Christopher T. Lee; Jeffrey Comer; Conner Herndon; Nelson Leung 003; Anna Pavlova; Robert V. Swift; Chris Tung; Christopher N. Rowley; Rommie E. Amaro; Christophe Chipot; Yi Wang; James C. Gumbart (J. Chem. Inf. Model., 2016)

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations. - Haohao Fu; James C. Gumbart; Haochuan Chen; Xueguang Shao; Wensheng Cai; Christophe Chipot (J. Chem. Inf. Model., 2018)

A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins. - Hyea Hwang; Anthony Hazel; Peng Lian; Jeremy C. Smith; James C. Gumbart; Jerry M. Parks (J. Comput. Chem., 2020)

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. - 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; et al. (J. Chem. Inf. Model., 2020)

Membrane thinning and lateral gating are consistent features of BamA across multiple species. - Jinchan Liu; James C. Gumbart (PLoS Comput. Biol., 2020)

Protein Structure Prediction in the 3D HP Model Using Deep Reinforcement Learning. - Giovanny Espitia; Yui Tik Pang; James C. Gumbart (CoRR, 2024)

Machine Learning of Molecular Dynamics Simulations Provides Insights into the Modulation of Viral Capsid Assembly. - Anna Pavlova; Zixing Fan; Diane L. Lynch; James C. Gumbart (J. Chem. Inf. Model., 2025)