John D. Chodera
TitreCitée parAnnée
Statistically optimal analysis of samples from multiple equilibrium states
MR Shirts, JD Chodera
The Journal of chemical physics 129, 124105, 2008
9692008
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
9102010
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
6732011
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
5802007
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
4332013
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
4112007
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
3712011
Markov state models of biomolecular conformational dynamics
JD Chodera, F Noé
Current opinion in structural biology 25, 135-144, 2014
3432014
Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design
JD Chodera, DL Mobley
Annual Reviews, 2013
3122013
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
2902007
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
2602008
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
2602007
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
248*2011
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
2372017
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
2342013
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
2312006
Long-time protein folding dynamics from short-time molecular dynamics simulations
JD Chodera, WC Swope, JW Pitera, KA Dill
Multiscale Modeling and Simulation 5 (4), 1214, 2006
2172006
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
1982015
The ribosome modulates nascent protein folding
CM Kaiser, DH Goldman, JD Chodera, I Tinoco, C Bustamante
Science 334 (6063), 1723-1727, 2011
1892011
Alchemical free energy calculations: Ready for prime time?
MR Shirts, DL Mobley, JD Chodera
Annual Reports in Computational Chemistry 3, 41-59, 2007
1862007
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