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John D. Chodera
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OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
P Eastman, J Swails, JD Chodera, RT McGibbon, Y Zhao, KA Beauchamp, ...
PLoS computational biology 13 (7), e1005659, 2017
17782017
Statistically optimal analysis of samples from multiple equilibrium states
MR Shirts, JD Chodera
The Journal of chemical physics 129, 124105, 2008
17182008
Current status of the AMOEBA polarizable force field
JW Ponder, C Wu, P Ren, VS Pande, JD Chodera, MJ Schnieders, ...
The Journal of Physical Chemistry B 114 (8), 2549-2564, 2010
14192010
Markov models of molecular kinetics: Generation and validation
JH Prinz, H Wu, M Sarich, B Keller, M Senne, M Held, JD Chodera, ...
The Journal of chemical physics 134, 174105, 2011
12162011
Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
JD Chodera, N Singhal, VS Pande, KA Dill, WC Swope
The Journal of chemical physics 126, 155101, 2007
7392007
Markov state models of biomolecular conformational dynamics
JD Chodera, F Noť
Current opinion in structural biology 25, 135-144, 2014
7182014
OpenMM 4: a reusable, extensible, hardware independent library for high performance molecular simulation
P Eastman, MS Friedrichs, JD Chodera, RJ Radmer, CM Bruns, JP Ku, ...
Journal of chemical theory and computation 9 (1), 461-469, 2013
6742013
Alchemical free energy methods for drug discovery: progress and challenges
JD Chodera, DL Mobley, MR Shirts, RW Dixon, K Branson, VS Pande
Current Opinion in Structural Biology, 2011
5872011
Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity
EC Thomson, LE Rosen, JG Shepherd, R Spreafico, A da Silva Filipe, ...
Cell 184 (5), 1171-1187. e20, 2021
5502021
Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations
JD Chodera, WC Swope, JW Pitera, C Seok, KA Dill
Journal of Chemical Theory and Computation 3 (1), 26-41, 2007
5352007
Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design
JD Chodera, DL Mobley
Annual review of biophysics 42, 121-142, 2013
5332013
Hypoxia induces production of L-2-hydroxyglutarate
AM Intlekofer, RG Dematteo, S Venneti, LWS Finley, C Lu, AR Judkins, ...
Cell metabolism 22 (2), 304-311, 2015
4472015
Ensemble docking in drug discovery
RE Amaro, J Baudry, J Chodera, ÷ Demir, JA McCammon, Y Miao, ...
Biophysical journal 114 (10), 2271-2278, 2018
3782018
SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape
TN Starr, N Czudnochowski, Z Liu, F Zatta, YJ Park, A Addetia, D Pinto, ...
Nature 597 (7874), 97-102, 2021
3612021
Systematic improvement of a classical molecular model of water
LP Wang, T Head-Gordon, JW Ponder, P Ren, JD Chodera, PK Eastman, ...
The Journal of Physical Chemistry B 117 (34), 9956-9972, 2013
3532013
The protein folding problem: when will it be solved?
KA Dill, SB Ozkan, TR Weikl, JD Chodera, VA Voelz
Current opinion in structural biology 17 (3), 342-346, 2007
3452007
Predicting absolute ligand binding free energies to a simple model site
DL Mobley, AP Graves, JD Chodera, AC McReynolds, BK Shoichet, ...
Journal of molecular biology 371 (4), 1118-1134, 2007
3332007
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
DL Mobley, JD Chodera, KA Dill
The Journal of chemical physics 125, 084902, 2006
3282006
Predicting small-molecule solvation free energies: an informal blind test for computational chemistry
A Nicholls, DL Mobley, JP Guthrie, JD Chodera, CI Bayly, MD Cooper, ...
Journal of medicinal chemistry 51 (4), 769-779, 2008
3222008
The ribosome modulates nascent protein folding
CM Kaiser, DH Goldman, JD Chodera, I Tinoco Jr, C Bustamante
Science 334 (6063), 1723-1727, 2011
3182011
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Articles 1–20