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1

The protein folding problem: when will it be solved?

Ken A Dill, S Banu Ozkan, Thomas R Weikl, John D Chodera, Vincent A Voelz

Journal:

Current Opinion in Structural Biology

Year:

2007

Language:

english

File:

PDF, 131 KB

english, 2007

2

Markov models of molecular kinetics: Generation and validation

Prinz, Jan-Hendrik, Wu, Hao, Sarich, Marco, Keller, Bettina, Senne, Martin, Held, Martin, Chodera, John D., Schütte, Christof, Noé, Frank

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 1.83 MB

english, 2011

3

Escaping atom types in force fields using direct chemical perception

Mobley, David L, Bannan, Caitlin Colleen, Rizzi, Andrea, Bayly, Christopher I., Chodera, John Damon, Lim, Victoria T, Lim, Nathan M., Beauchamp, Kyle A., Slochower, David R, Shirts, Michael R., Eastma

Journal:

Journal of Chemical Theory and Computation

Year:

2018

Language:

english

File:

PDF, 2.58 MB

english, 2018

4

OpenPathSampling: A Python framework for path sampling simulations. I. Basics

Swenson, David, Prinz, Jan-Hendrik, Noé, Frank, Chodera, John Damon, Bolhuis, Peter G.

Journal:

Journal of Chemical Theory and Computation

Year:

2018

Language:

english

File:

PDF, 2.65 MB

english, 2018

5

OpenPathSampling: A Python framework for path sampling simulations. II. Building and customizing path ensembles and sample schemes

Swenson, David, Prinz, Jan-Hendrik, Noé, Frank, Chodera, John Damon, Bolhuis, Peter G.

Journal:

Journal of Chemical Theory and Computation

Year:

2018

Language:

english

File:

PDF, 4.81 MB

english, 2018

6

Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

Chodera, John D., Mobley, David L.

Journal:

Annual Review of Biophysics

Year:

2013

Language:

english

File:

PDF, 532 KB

english, 2013

7

Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

Wang, Kai, Chodera, John D., Yang, Yanzhi, Shirts, Michael R.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2013

Language:

english

File:

PDF, 856 KB

english, 2013

8

A simple method for automated equilibration detection in molecular simulations

Chodera, John Damon

Journal:

Journal of Chemical Theory and Computation

Year:

2016

Language:

english

File:

PDF, 870 KB

english, 2016

9

Conformational Dynamics of Histone Lysine Methyltransferases by Millisecond-Timescale Molecular Dynamics on Folding@home

Wiewiora, Rafal P., Chen, Shi, Beauchamp, Kyle, Luo, Minkui, Chodera, John D.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 49 KB

english, 2017

10

Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations

Hauser, Kevin, Negron, Christopher, Albanese, Steven K., Ray, Soumya, Steinbrecher, Thomas, Abel, Robert, Chodera, John D., Wang, Lingle

Journal:

Communications Biology

Year:

2018

Language:

english

File:

PDF, 1.57 MB

english, 2018

11

Is Structure-Based Drug Design Ready for Selectivity Optimization?

Albanese, Steven K., Chodera, John D., Volkamer, Andrea, Keng, Simon, Abel, Robert, Wang, Lingle

Journal:

Journal of Chemical Information and Modeling

Year:

2020

File:

PDF, 4.90 MB

2020

12

MOPED: Method for optimizing physical energy parameters using decoys

Chaok Seok, J. B. Rosen, John D. Chodera, Ken A. Dill

Journal:

Journal of Computational Chemistry

Year:

2003

Language:

english

File:

PDF, 145 KB

english, 2003

13

Systematic errors in isothermal titration calorimetry: Concentrations and baselines

Joel Tellinghuisen, John D. Chodera

Journal:

Analytical Biochemistry

Year:

2011

Language:

english

File:

PDF, 375 KB

english, 2011

14

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

Mobley, David L., Chodera, John D., Dill, Ken A.

Journal:

The Journal of Chemical Physics

Year:

2006

Language:

english

File:

PDF, 1.04 MB

english, 2006

15

Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing

Chodera, John D., Shirts, Michael R.

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 1.14 MB

english, 2011

16

Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change

Mobley, David L., Chodera, John D., Dill, Ken A.

Journal:

Journal of Chemical Theory and Computation

Year:

2007

Language:

english

File:

PDF, 143 KB

english, 2007

17

Alchemical free energy methods for drug discovery: progress and challenges

John D Chodera, David L Mobley, Michael R Shirts, Richard W Dixon, Kim Branson, Vijay S Pande

Journal:

Current Opinion in Structural Biology

Year:

2011

Language:

english

File:

PDF, 222 KB

english, 2011

18

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, Ken A. Dill

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 955 KB

english, 2007

19

Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations

Chodera, John D., Swope, William C., Pitera, Jed W., Dill, Ken A.

Journal:

Multiscale Modeling and Simulation

Year:

2006

Language:

english

File:

PDF, 677 KB

english, 2006

20

Treating Entropy and Conformational Changes in Implicit Solvent Simulations of Small Molecules

Mobley, David L., Dill, Ken A., Chodera, John D.

Journal:

Journal of Physical Chemistry B

Year:

2008

Language:

english

File:

PDF, 200 KB

english, 2008

21

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

Eastman, Peter, Friedrichs, Mark S., Chodera, John D., Radmer, Randall J., Bruns, Christopher M., Ku, Joy P., Beauchamp, Kyle A., Lane, Thomas J., Wang, Lee-Ping, Shukla, Diwakar, Tye, Tony, Houston,

Journal:

Journal of Chemical Theory and Computation

Year:

2013

Language:

english

File:

PDF, 323 KB

english, 2013

22

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

Chodera, John D., Singhal, Nina, Pande, Vijay S., Dill, Ken A., Swope, William C.

Journal:

The Journal of Chemical Physics

Year:

2007

Language:

english

File:

PDF, 1.97 MB

english, 2007

23

Comparison of Charge Models for Fixed-Charge Force Fields: Small-Molecule Hydration Free Energies in Explicit Solvent

Mobley, David L., Dumont, Élise, Chodera, John D., Dill, Ken A.

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 394 KB

english, 2007

24

The Mechanical Properties of PCNA: Implications for the Loading and Function of a DNA Sliding Clamp

Adelman, Joshua L., Chodera, John D., Kuo, I-Feng W., Miller, Thomas F., Barsky, Daniel

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 761 KB

english, 2010

25

Limitations of Constant-Force-Feedback Experiments

Elms, Phillip J., Chodera, John D., Bustamante, Carlos J., Marqusee, Susan

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 1.00 MB

english, 2012

26

Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry

Nicholls, Anthony, Mobley, David L., Guthrie, J. Peter, Chodera, John D., Bayly, Christopher I., Cooper, Matthew D., Pande, Vijay S.

Journal:

Journal of Medicinal Chemistry

Year:

2008

Language:

english

File:

PDF, 1.55 MB

english, 2008

27

Splitting Probabilities as a Test of Reaction Coordinate Choice in Single-Molecule Experiments

Chodera, John D., Pande, Vijay S.

Journal:

Physical Review Letters

Year:

2011

Language:

english

File:

PDF, 347 KB

english, 2011

28

Statistically optimal analysis of samples from multiple equilibrium states

Shirts, Michael R., Chodera, John D.

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 450 KB

english, 2008

29

Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolution

Chodera, John D., Noé, Frank

Journal:

The Journal of Chemical Physics

Year:

2010

Language:

english

File:

PDF, 699 KB

english, 2010

30

Systematic Improvement of a Classical Molecular Model of Water

Wang, Lee-Ping, Head-Gordon, Teresa, Ponder, Jay W., Ren, Pengyu, Chodera, John D., Eastman, Peter K., Martinez, Todd J., Pande, Vijay S.

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 2.91 MB

english, 2013

31

Acknowledgement to referees

Wang, Kai, Chodera, John D., Yang, Yanzhi, Shirts, Michael R.

Journal:

Archives of Toxicology

Year:

2014

File:

PDF, 98 KB

2014

32

The Mechanical Properties of PCNA: Implications for the Loading and Function of Sliding Clamps

Adelman, Joshua L., Chodera, John D., Kuo, I-Feng W., Miller, Thomas F., Barsky, Daniel

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 31 KB

english, 2010

33

Toward a Global View of the Conformational Landscape of the Human Kinome

Parton, Daniel L., Shukla, Diwakar, Zhao, Yutong, Pande, Vijay S., Chodera, John D.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 98 KB

english, 2014

34

Numerical Langevin Simulations: Equilibrium Dynamics and Nonequilibrium Thermodynamics

Sivak, David A., Chodera, John D., Crooks, Gavin E.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 57 KB

english, 2014

35

Systematic Improvement on the Classical Molecular Model of Water

Wang, Lee-Ping, Head-Gordon, Teresa, Ponder, Jay, Ren, Pengyu, Chodera, John, Eastman, Peter, Martinez, Todd J., Pande, Vijay S.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 57 KB

english, 2014

36

Markov state models of biomolecular conformational dynamics

Chodera, John D, Noé, Frank

Journal:

Current Opinion in Structural Biology

Year:

2014

Language:

english

File:

PDF, 566 KB

english, 2014

37

Accurate and Efficient Corrections for Missing Dispersion Interactions in Molecular Simulations

Shirts, Michael R., Mobley, David L., Chodera, John D., Pande, Vijay S.

Journal:

Journal of Physical Chemistry B

Year:

2007

Language:

english

File:

PDF, 112 KB

english, 2007

38

Current Status of the AMOEBA Polarizable Force Field

Ponder, Jay W., Wu, Chuanjie, Ren, Pengyu, Pande, Vijay S., Chodera, John D., Schnieders, Michael J., Haque, Imran, Mobley, David L., Lambrecht, Daniel S., DiStasio, Robert A., Head-Gordon, Martin, Cl

Journal:

Journal of Physical Chemistry B

Year:

2010

Language:

english

File:

PDF, 623 KB

english, 2010

39

Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems

Sivak, David A., Chodera, John D., Crooks, Gavin E.

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 495 KB

english, 2014

40

Comparison of Charge Models for Fixed-Charge Force Fields: Small Molecule Hydration Free Energies in Explicit Solvent

Mobley, David L., Dumont, Élise, Chodera, John D., Dill, Ken A.

Journal:

Journal of Physical Chemistry B

Year:

2011

Language:

english

File:

PDF, 837 KB

english, 2011

41

On the Use of Experimental Observations to Bias Simulated Ensembles

Pitera, Jed W., Chodera, John D.

Journal:

Journal of Chemical Theory and Computation

Year:

2012

Language:

english

File:

PDF, 952 KB

english, 2012

42

An Alternative Explanation for the Catalytic Proficiency of Orotidine 5‘-Phosphate Decarboxylase

Lee, Tai-Sung, Chong, Lillian T., Chodera, John D., Kollman, Peter A.

Journal:

Journal of the American Chemical Society

Year:

2001

Language:

english

File:

PDF, 153 KB

english, 2001

43

Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

Chodera, John D., Swope, William C., Pitera, Jed W., Seok, Chaok, Dill, Ken A.

Journal:

Journal of Chemical Theory and Computation

Year:

2007

Language:

english

File:

PDF, 165 KB

english, 2007

44

Erratum: “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” [J. Chem. Phys. 134, 024111 (2011)]

Minh, David D. L., Chodera, John D.

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 309 KB

english, 2012

45

Using Nonequilibrium Fluctuation Theorems to Understand and Correct Errors in Equilibrium and Nonequilibrium Simulations of Discrete Langevin Dynamics

Sivak, David A., Chodera, John D., Crooks, Gavin E.

Journal:

Physical Review X

Year:

2013

Language:

english

File:

PDF, 346 KB

english, 2013

46

Spectral Rate Theory for Two-State Kinetics

Prinz, Jan-Hendrik, Chodera, John D., Noé, Frank

Journal:

Physical Review X

Year:

2014

Language:

english

File:

PDF, 3.21 MB

english, 2014

47

Erratum: Splitting Probabilities as a Test of Reaction Coordinate Choice in Single-Molecule Experiments [Phys. Rev. Lett. 107 , 098102 (2011)]

Chodera, John D., Pande, Vijay S.

Journal:

Physical Review Letters

Year:

2012

Language:

english

File:

PDF, 28 KB

english, 2012

48

Dynamical reweighting: Improved estimates of dynamical properties from simulations at multiple temperatures

Chodera, John D., Swope, William C., Noé, Frank, Prinz, Jan-Hendrik, Shirts, Michael R., Pande, Vijay S.

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 762 KB

english, 2011

49

Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages

Minh, David D. L., Chodera, John D.

Journal:

The Journal of Chemical Physics

Year:

2009

Language:

english

File:

PDF, 625 KB

english, 2009

50

Hypoxia Induces Production of L-2-Hydroxyglutarate

Intlekofer, Andrew M., Dematteo, Raymond G., Venneti, Sriram, Finley, Lydia W.S., Lu, Chao, Judkins, Alexander R., Rustenburg, Ariën S., Grinaway, Patrick B., Chodera, John D., Cross, Justin R., Thomp

Journal:

Cell Metabolism

Year:

2015

Language:

english

File:

PDF, 1.54 MB

english, 2015