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Journal Articles
- 2020
[j10]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): 528-537 (2020)- [j9]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:
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19. J. Chem. Inf. Model. 60(12): 5832-5852 (2020) - [j8]Jinchan Liu, James C. Gumbart:
Membrane thinning and lateral gating are consistent features of BamA across multiple species. PLoS Comput. Biol. 16(10) (2020) - 2018
- [j7]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): 556-560 (2018) - 2016
- [j6]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): 721-733 (2016) - 2015
- [j5]Anna Pavlova, James C. Gumbart:
Parametrization of macrolide antibiotics using the force field toolkit. J. Comput. Chem. 36(27): 2052-2063 (2015) - 2014
- [j4]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): 908-916 (2014) - [j3]James C. Gumbart, Morgan Beeby, Grant J. Jensen, Benoît Roux:
Escherichia coli Peptidoglycan Structure and Mechanics as Predicted by Atomic-Scale Simulations. PLoS Comput. Biol. 10(2) (2014) - 2013
- [j2]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): 2757-2770 (2013) - 2005
- [j1]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): 1781-1802 (2005)
Conference and Workshop Papers
- 2012
- [c1]Fatemeh Khalili-Araghi, Brigitte Ziervogel, Benoît Roux, James C. Gumbart:
Membrane protein simulations under asymmetric ionic concentrations. XSEDE 2012: 16:1
Coauthor Index
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