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51

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

Bacallado, Sergio, Chodera, John D., Pande, Vijay

Journal:

The Journal of Chemical Physics

Year:

2009

Language:

english

File:

PDF, 264 KB

english, 2009

52

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

53

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

54

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

55

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

56

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

57

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

58

Bridging the Gap between Computation and Experiments in GPCRs

Stern, Chaya D., Perez-Aguilar, Jose M., Blanchard, Scott C., Weinstein, Harel, Chodera, John D.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 60 KB

english, 2016

59

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

60

Benchmarking and Optimizing Atomistic Forcefields with Density Measurements

Beauchamp, Kyle A., Behr, Julie M., Grinaway, Patrick B., Rustenburg, Arien S., Chodera, John D.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 55 KB

english, 2015

61

Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies

Hanson, Sonya M., Ekins, Sean, Chodera, John D.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2015

Language:

english

File:

PDF, 1.60 MB

english, 2015

62

Introduction to the special issue: Data Part 2: Experimental Data

Kramer, Christian, Chodera, John, Stouch, Terry

Journal:

Journal of Computer-Aided Molecular Design

Year:

2015

Language:

english

File:

PDF, 287 KB

english, 2015

63

Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge

Rustenburg, Ariën S., Dancer, Justin, Lin, Baiwei, Feng, Jianwen A., Ortwine, Daniel F., Mobley, David L., Chodera, John D.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2016

Language:

english

File:

PDF, 942 KB

english, 2016

64

NIH Public Access

Chodera, John D, Mobley, David L

Year:

2014

Language:

english

File:

PDF, 1.29 MB

english, 2014

65

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

66

L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH

Intlekofer, Andrew M, Wang, Bo, Liu, Hui, Shah, Hardik, Carmona-Fontaine, Carlos, Rustenburg, Ariën S, Salah, Salah, Gunner, M R, Chodera, John D, Cross, Justin R, Thompson, Craig B

Journal:

Nature Chemical Biology

Year:

2017

Language:

english

File:

PDF, 1.16 MB

english, 2017

67

Can we Automatically Detect Biologically Relevant Order Parameters in Molecular Simulation? Comparing Long Timescale Simulations of Multiple Kinases

Hanson, Sonya M., Fass, Joshua H., Chodera, John D.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 46 KB

english, 2017

68

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics

Prinz, Jan-Hendrik, Chodera, John D., Pande, Vijay S., Swope, William C., Smith, Jeremy C., Noé, Frank

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 1.13 MB

english, 2011

69

Approaches for Calculating Solvation Free Energies and Enthalpies Demonstrated with an Update of the FreeSolv Database

Duarte Ramos Matos, Guilherme, Kyu, Daisy Y., Loeffler, Hannes H., Chodera, John D., Shirts, Michael R., Mobley, David L.

Journal:

Journal of Chemical & Engineering Data

Year:

2017

Language:

english

File:

PDF, 1.40 MB

english, 2017

70

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

71

Ensemble Docking in Drug Discovery

Amaro, Rommie E., Baudry, Jerome, Chodera, John, Demir, Özlem, McCammon, J. Andrew, Miao, Yinglong, Smith, Jeremy C.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 659 KB

english, 2018

72

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

73

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Eastman, Peter, Swails, Jason, Chodera, John D., McGibbon, Robert T., Zhao, Yutong, Beauchamp, Kyle A., Wang, Lee-Ping, Simmonett, Andrew C., Harrigan, Matthew P., Stern, Chaya D., Wiewiora, Rafal P.,

Journal:

PLoS Computational Biology

Year:

2017

Language:

english

File:

PDF, 1.28 MB

english, 2017

74

A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation

Ruff, Emily F, Muretta, Joseph M, Thompson, Andrew R, Lake, Eric W, Cyphers, Soreen, Albanese, Steven K, Hanson, Sonya M, Behr, Julie M, Thomas, David D, Chodera, John D, Levinson, Nicholas M

Journal:

Year:

2018

Language:

english

File:

PDF, 2.34 MB

english, 2018

75

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

76

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

77

Overview of the SAMPL6 host–guest binding affinity prediction challenge

Rizzi, Andrea, Murkli, Steven, McNeill, John N., Yao, Wei, Sullivan, Matthew, Gilson, Michael K., Chiu, Michael W., Isaacs, Lyle, Gibb, Bruce C., Mobley, David L., Chodera, John D.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2018

Language:

english

File:

PDF, 4.61 MB

english, 2018

78

Toward learned chemical perception of force field typing rules

Zanette, Camila, Bannan, Caitlin Colleen, Bayly, Christopher I., Fass, Josh, Gilson, Michael K., Shirts, Michael R., Chodera, John Damon, Mobley, David L

Journal:

Journal of Chemical Theory and Computation

Year:

2018

Language:

english

File:

PDF, 1.89 MB

english, 2018

79

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

80

Sharing Data from Molecular Simulations

Abraham, Mark James, Apostolov, Rossen Pavlov, Barnoud, Jonathan, Bauer, Paul, Blau, Christian, Bonvin, Alexandre M.J.J., Chavent, Matthieu, Chodera, John Damon, Čondić-Jurkić, Karmen, Delemotte, Luci

Journal:

Journal of Chemical Information and Modeling

Year:

2019

Language:

english

File:

PDF, 1.51 MB

english, 2019

81

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

82

Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states

Gunner, M. R., Murakami, Taichi, Rustenburg, AriÃ«n S., IÅÄ±k, Mehtap, Chodera, John D.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2020

File:

PDF, 1.01 MB

2020

83

Assessing the accuracy of octanolâwater partition coefficient predictions in the SAMPL6 Part II logÂ P Challenge

IÅÄ±k, Mehtap, Bergazin, Teresa Danielle, Fox, Thomas, Rizzi, Andrea, Chodera, John D., Mobley, David L.

Journal:

Journal of Computer-Aided Molecular Design

Year:

2020

Language:

english

File:

PDF, 2.88 MB

english, 2020

84

Crowdsourcing drug discovery for pandemics

Chodera, John, Lee, Alpha A., London, Nir, von Delft, Frank

Journal:

Nature Chemistry

Year:

2020

File:

PDF, 735 KB

2020

85

Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems

Gkeka, Paraskevi, Stoltz, Gabriel, Barati Farimani, Amir, Belkacemi, Zineb, Ceriotti, Michele, Chodera, John Damon, Dinner, Aaron R, Ferguson, Andrew L., Maillet, Jean-Bernard, Minoux, Herve, Peter, C

Journal:

Journal of Chemical Theory and Computation

Year:

2020

File:

PDF, 3.03 MB

2020