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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

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

3

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

4

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

5

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

6

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

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

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

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

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

11

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

12

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

13

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

14

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo

Gill, Samuel C., Lim, Nathan M., Grinaway, Patrick B., Rustenburg, Ariën S., Fass, Josh, Ross, Gregory A., Chodera, John Damon, Mobley, David L

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 3.19 MB

english, 2018

15

Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

Nguyen, Trung Hai, Rustenburg, Ariën S., Krimmer, Stefan G., Zhang, Hexi, Clark, John D., Novick, Paul A., Branson, Kim, Pande, Vijay S., Chodera, John D., Minh, David D. L., Permyakov, Eugene A.

Journal:

Year:

2018

Language:

english

File:

PDF, 6.99 MB

english, 2018

16

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

17

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

18

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

19

Conformational Dynamics of Histone Methyltransferase SET8 Probed by Millisecond-Timescale Molecular Dynamics, Markov State Modeling and Biochemical Experiments

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

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 43 KB

english, 2018

20

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

21

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

22

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

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

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 1.17 MB

english, 2011

23

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

24

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

25

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

Beauchamp, Kyle A., Behr, Julie M., Rustenburg, Ariën S., Bayly, Christopher I., Kroenlein, Kenneth, Chodera, John D.

Journal:

Journal of Physical Chemistry B

Year:

2015

Language:

english

File:

PDF, 759 KB

english, 2015

26

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

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 531 KB

english, 2011

27

A water-mediated allosteric network governs activation of Aurora kinase A

Cyphers, Soreen, Ruff, Emily F, Behr, Julie M, Chodera, John D, Levinson, Nicholas M

Journal:

Nature Chemical Biology

Year:

2017

Language:

english

File:

PDF, 1.48 MB

english, 2017

28

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

29

The social network (of protein conformations)

John D. Chodera and Vijay S. Pande

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 581 KB

english, 2011

30

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

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

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

33

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

34

Simulating mTOR Hyperactivating Mutations to Understand Functionally Significant Structural Rearrangements

Albanese, Steven, Xu, Jianing, Hsieh, James, Chodera, John D.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 42 KB

english, 2016

35

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

36

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

37

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

38

Biomolecular Simulations Under Realistic Macroscopic Salt Conditions

Ross, Gregory A., Rustenburg, Ariën S., Grinaway, Patrick B., Fass, Josh, Chodera, John Damon

Journal:

Journal of Physical Chemistry B

Year:

2018

Language:

english

File:

PDF, 4.53 MB

english, 2018

39

What Makes a Kinase Promiscuous for Inhibitors?

Hanson, Sonya M., Georghiou, George, Thakur, Manish K., Miller, W. Todd, Rest, Joshua S., Chodera, John D., Seeliger, Markus A.

Journal:

Cell Chemical Biology

Year:

2019

Language:

english

File:

PDF, 3.35 MB

english, 2019

40

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

Frank Noé, Sören Doose, Isabella Daidone, Marc Löllmann, Markus Sauer, John D. Chodera, Jeremy C. Smith and William A. Eaton

Journal:

Proceedings of the National Academy of Sciences

Year:

2011

Language:

english

File:

PDF, 1.53 MB

english, 2011

41

Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

Slochower, David R, Henriksen, Niel M., Wang, Lee-Ping, Chodera, John Damon, Mobley, David L, Gilson, Michael

Journal:

Journal of Chemical Theory and Computation

Year:

2019

Language:

english

File:

PDF, 2.76 MB

english, 2019

42

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

43

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

44

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

45

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

46

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

47

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

48

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

49

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

50

Developing High-Throughput Fluorescence-Based Assays for Measuring Kinase Inhibitor Free Energies of Binding

Hanson, Sonya M., Prinz, Jan-Hendrik, Behr, Julie M., Grinaway, Patrick B., Rustenburg, Arien S., Beauchamp, Kyle A., Parton, Daniel L., Chodera, John D.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 42 KB

english, 2015

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