Publications

The role of blanks in isothermal titration calorimetry
Joel T. Tellinghuisen, Sarah E. Boyce, and John D. Chodera.
Submitted (2012)

On the use of experimental observations to bias simulated ensembles
Jed W. Pitera and John D. Chodera.
Submitted (2012)

A robust approach to estimating rates from time-correlation functions
John D. Chodera Phillip J. Elms, William C. Swope, Jan-Hendrik Prinz, Susan Marqusee, Carlos Bustamante, Frank Noé, and Vijay S. Pande.
Submitted (2011)

Bayesian hidden Markov model analysis of single-molecule biophysical experimens: Characterizing metastable states and transition rates under measurement uncertainty
John D. Chodera, Phillip J. Elms, Frank Noé, Bettina Keller, Christian M. Kaiser, Aaron Ewall-Wice, Susan Marqusee, Carlos J. Bustamante, and Nina Singhal Hinrichs.
Submitted (2011)

Driven Langevin dynamics: heat, work, and pseudo-work
David A. Sivak, John D. Chodera, and Gavin E. Crooks.
Submitted (2011)

Equilibrium force spectroscopy experiments: The difference between constant force feedback and constant trap position experiments.
Phillip Elms, John D. Chodera, Carlos Bustamante, and Susan Marqusee.
Submitted (2011)

The molten globule state is unusually deformable under mechanical force
Phillip J. Elms, John D. Chodera, Carlos Bustamante, and Susan Marqusee.
Proc. Natl. Acad. Sci. USA, 109:3796 (2012)

The ribosome modulates nascent protein folding
Christian Kaiser, Daniel H. Goldman, John D. Chodera, Ignacio Tinoco, Jr., and Carlos Bustamante.
Science 334:1723 (2011)

Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing
John D. Chodera and Michael R. Shirts.
J. Chem. Phys. 135:194110 (2011)

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation
Jerome P. Nilmeier, Gavin E. Crooks, David D. L. Minh, and John D. Chodera.
Proc. Natl. Acad. Sci. USA, 108:E1009 (2011)

PNAS Commentary: The social network (of protein conformations)
John D. Chodera and Vijay S. Pande.
Proc. Natl. Acad. Sci. USA, 108:12969-12970 (2011)

Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments
John D. Chodera and Vijay S. Pande.
Phys. Rev. Lett., 107:098102 (2011)

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics
Jan-Hendrik Prinz, John D. Chodera, Vijay S. Pande, William C. Swope, Jeremy C. Smith, and Frank Noé
J. Chem. Phys., 134:244108 (2011)

Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures
John D. Chodera, William C. Swope, Frank Noé, Jan-Hendrik Prinz, Michael R. Shirts, and Vijay S. Pande
J. Chem. Phys., 134:244107 (2011)

Systematic errors in isothermal titration calorimetry: Concentrations and baselines
Joel T. Tellinghuisen and John D. Chodera.
Anal. Biochem., 414:297 (2011)

Markov models of molecular kinetics: Generation and validation
Jan-Hendrik Prinz, Hao Wu, Marco Sarich, Bettina Keller, Martin Fischbach, Martin Held, John D. Chodera, Christof Schütte, and Frank Noé,
J. Chem. Phys., 134:174105 (2011)

Free energy methods in drug discovery and design: Progress and challenges
John D. Chodera, David L. Mobley, Michael R. Shirts, Richard W. Dixon Kim M. Branson, and Vijay S. Pande.
Curr. Opin. Struct. Biol., 21:150 (2011)

Dynamical fingerprints: A theoretical framework for understanding biomolecular processes by combination of simulation and kinetic experiments
Frank Noé, Sören Doose, Isabella Daidone, Marc Löllmann, Markus Sauer, John D. Chodera, and Jeremy C. Smith
Proc. Natl. Acad. Sci. USA 108:4822 (2011)

Estimating equilibrium ensemble averages using multiple time slices from driven nonequilibrium processes: theory and application to free energies, moments, and thermodynamic length in single-molecule pulling experiments
David D. L. Minh and John D. Chodera
J. Chem. Phys. 134:024111 (2011)

Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolution
John D. Chodera and Frank Noé
J. Chem. Phys. 133:105102 (2010)

The mechanical properties of PCNA: Implications for the loading and function of a DNA sliding clamp
Joshua L. Adelman, John D. Chodera, I-Feng W. Kuo, Thomas F. Miller, and Daniel Barsky
Biophys. J. 98:3062 (2010)

Current status of the AMOEBA polarizable force field
Jay W. Ponder, Chuanjie Wu, Pengyu Ren, Vijay S. Pande, John D. Chodera, David L. Mobley, Michael J. Schnieders, Imran Haque, D. S. Lambrecht, R. A. DiStasio, Jr., Martin Head-Gordon, Gary N. I. Clark, Margaret E. Johnson, and Teresa Head-Gordon.
J. Phys. Chem. B 114:2549 (2010)

Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages
David D. L. Minh and John D. Chodera.
J. Chem. Phys. 131:134110 (2009)

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint
Sergio Bacallado, John D. Chodera, and Vijay S. Pande.
J. Chem. Phys. 131:045106 (2009)

Statistically optimal analysis of samples from multiple equilibrium states
Michael R. Shirts and John D. Chodera.
J. Chem. Phys. 129:124105 (2008)

Predicting small-molecule solvation free energies: a blind challenge test for computational chemistry
Anthony Nicholls*, David L. Mobley*, J. Peter Guthrie, John D. Chodera, and Vijay S. Pande.
* These authors contributed equally to this work.
J. Med. Chem. 51(4):769-779 (2008)

Treating entropy and conformational changes in implicit solvent simulations of small molecules
David L. Mobley, Ken A. Dill, and John D. Chodera.
J. Phys. Chem. B, 112(3):938-946 (2008)

Alchemical free energy calculations: Ready for prime time?
Michael R. Shirts, David L. Mobley, and John D. Chodera.
Annu. Rep. Comput. Chem., 3:41-59 (2007)

Accurate and efficient corrections for missing dispersion interactions in molecular simulations
Michael R. Shirts, David L. Mobley, John D. Chodera, and Vijay S. Pande.
J. Phys. Chem. B, 111(45):13052-13063 (2007)

Protein Folding by Zipping and Assembly
S. Banu Ozkan, G. Albert Wu, John D. Chodera, and Ken A. Dill.
Proc. Natl. Acad. Sci. USA, 104(29):11987-11992 (2007)

Predicting absolute ligand binding free energies to a simple model site
David L. Mobley*, Alan P. Graves*, John D. Chodera, Andrea C. McReynolds, Brian K. Shoichet, and Ken A. Dill.
* These authors contributed equally to the work.
J. Mol. Biol., 371(4):1118-1134 (2007)

The protein folding problem: When will it be solved?
Ken A. Dill, S. Banu Ozkan, Thomas R. Weikl, John D. Chodera, and Vincent A. Voelz.
Curr. Opin. Struct. Biol., 17(3):342-346 (2007)

Confine-and-release method: Obtaining correct binding free energies in the presence of protein conformational change
David L. Mobley, John D. Chodera, and Ken A. Dill.
J. Chem. Theor. Comput. 3(4):1231-1235 (2007)

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
John D. Chodera*, Nina Singhal*, William C. Swope, Vijay S. Pande, and Ken A. Dill.
* These authors contributed equally to the work.
J. Chem. Phys. 126(15):155101 (2007)

Comparison of charge models for fixed-charge forcefields: Small molecule hydration free energies in explicit solvent
David L. Mobley, Elise Dumont, John D. Chodera, and Ken A. Dill.
J. Phys. Chem. B 111(9):2242-2254 (2007)

Long-time protein folding dynamics from short-time molecular dynamics simulations
John D. Chodera, William C. Swope, Jed W. Pitera, and Ken A. Dill.
Multiscale Modeling & Simulation, Special Section on Multiscale Modeling in Biology, 5(4):1214-1226 (2006)

Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations
John D. Chodera, William C. Swope, Jed W. Pitera, Chaok Seok, and Ken A. Dill.
J. Chem. Theor. Comput. 3(1):26-41 (2007)

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
David L. Mobley, John D. Chodera, and Ken A. Dill.
J. Chem. Phys. 125(8):084902 (2006)

MOPED: Method for optimizing physical energy parameters using decoys
Chaok Seok, J. B. Rosen, John D. Chodera, and Ken A. Dill.
J. Comput. Chem., 24(1):89-97 (2003)

An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase
Tai-Sung Lee*, Lillian T. Chong*, John D. Chodera, and Peter A. Kollman.
* These authors contributed equally to the work.
J. Am. Chem. Soc., 123(51):12837-12848 (2001)