James C. Gumbart

According to our database, James C. Gumbart authored at least 12 papers between 2005 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Protein Structure Prediction in the 3D HP Model Using Deep Reinforcement Learning.

Giovanny Espitia, Yui Tik Pang, James C. Gumbart

CoRR, 2024

2020

Membrane thinning and lateral gating are consistent features of BamA across multiple species.

Jinchan Liu, James C. Gumbart

PLoS Comput. Biol., 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, 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

J. Chem. Inf. Model., 2020

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

2018

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

2016

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds.

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

J. Chem. Inf. Model., 2016

2015

Parametrization of macrolide antibiotics using the force field toolkit.

Anna Pavlova, James C. Gumbart

J. Comput. Chem., 2015

2014

<i>Escherichia coli</i> Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations.

James C. Gumbart, Morgan Beeby, Grant J. Jensen, Benoît Roux

PLoS Comput. Biol., 2014

Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD.

Wei Jiang, James C. Phillips, Lei Huang, Mikolai Fajer, Yilin Meng, James C. Gumbart, Yun Luo, Klaus Schulten, Benoît Roux

Comput. Phys. Commun., 2014

2013

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

2012

Membrane protein simulations under asymmetric ionic concentrations.

Fatemeh Khalili-Araghi, Brigitte Ziervogel, Benoît Roux, James C. Gumbart

Proceedings of the 1st Conference of the Extreme Science and Engineering Discovery Environment, 2012

2005

Scalable molecular dynamics with NAMD.

James C. Phillips, Rosemary Braun, Wei Wang, James C. Gumbart, Emad Tajkhorshid, Elizabeth Villa, Christophe Chipot, Robert D. Skeel, Laxmikant V. Kalé, Klaus Schulten

J. Comput. Chem., 2005