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John D. Chodera
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Statistically optimal analysis of samples from multiple equilibrium states
MR Shirts, JD Chodera
The Journal of chemical physics 129, 124105, 2008
14162008
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
12142010
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
10252011
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
10182017
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
6822007
Markov state models of biomolecular conformational dynamics
JD Chodera, F Noť
Current opinion in structural biology 25, 135-144, 2014
5952014
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
5702013
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
5072011
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
4892007
Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design
JD Chodera, DL Mobley
Annual review of biophysics 42, 121, 2013
4442013
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
4142021
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
3572015
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
3262007
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
3092013
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
3062008
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
3052007
Comparison of Charge Models for Fixed-Charge Force Fields: Small Molecule Hydration Free Energies in Explicit Solvent
DL Mobley, E Dumont, JD Chodera, KA Dill
The journal of physical chemistry. B 115 (5), 1329-1332, 2011
290*2011
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
2902006
The ribosome modulates nascent protein folding
CM Kaiser, DH Goldman, JD Chodera, I Tinoco Jr, C Bustamante
Science 334 (6063), 1723-1727, 2011
2662011
Ensemble docking in drug discovery
RE Amaro, J Baudry, J Chodera, ÷ Demir, JA McCammon, Y Miao, ...
Biophysical journal 114 (10), 2271-2278, 2018
2652018
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Articles 1–20