John D. Chodera
Title
Cited by
Cited by
Year
Statistically optimal analysis of samples from multiple equilibrium states
MR Shirts, JD Chodera
The Journal of chemical physics 129, 124105, 2008
11112008
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
10052010
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
7892011
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
6182007
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
4882013
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
4312007
Markov state models of biomolecular conformational dynamics
JD Chodera, F Noť
Current opinion in structural biology 25, 135-144, 2014
4302014
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
4292017
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
4192011
Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design
JD Chodera, DL Mobley
Annual Reviews, 2013
3562013
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
3022007
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
2762007
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
2752008
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
2632013
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
260*2011
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
2512015
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
2492006
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
2282006
The ribosome modulates nascent protein folding
CM Kaiser, DH Goldman, JD Chodera, I Tinoco, C Bustamante
Science 334 (6063), 1723-1727, 2011
2182011
Alchemical free energy calculations: Ready for prime time?
MR Shirts, DL Mobley, JD Chodera
Annual Reports in Computational Chemistry 3, 41-59, 2007
2102007
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Articles 1–20