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John D. Chodera, Ph.D. - Publications

Affiliations: 
1999-2006 Graduate Group in Biophysics University of California, San Francisco, San Francisco, CA 
 2007-2008 Chemistry Stanford University, Palo Alto, CA 
 2008-2012 QB3 University of California, Berkeley, Berkeley, CA, United States 
 2012- Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center, Rockville Centre, NY, United States 
Area:
drug discovery, computational biophysics, protein folding and stability
Website:
http://choderalab.org
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117 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Zhang I, Rufa DA, Pulido I, Henry MM, Rosen LE, Hauser K, Singh S, Chodera JD. Correction to Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex. Journal of Chemical Theory and Computation. PMID 38164914 DOI: 10.1021/acs.jctc.3c01298  0.439
2023 Eastman P, Galvelis R, Peláez RP, Abreu CRA, Farr SE, Gallicchio E, Gorenko A, Henry MM, Hu F, Huang J, Krämer A, Michel J, Mitchell JA, Pande VS, Rodrigues JP, ... ... Chodera JD, et al. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. The Journal of Physical Chemistry. B. PMID 38154096 DOI: 10.1021/acs.jpcb.3c06662  0.593
2023 Outhwaite IR, Singh S, Berger BT, Knapp S, Chodera JD, Seeliger MA. Death by a thousand cuts through kinase inhibitor combinations that maximize selectivity and enable rational multitargeting. Elife. 12. PMID 38047771 DOI: 10.7554/eLife.86189  0.646
2023 Eastman P, Galvelis R, Peláez RP, Abreu CRA, Farr SE, Gallicchio E, Gorenko A, Henry MM, Hu F, Huang J, Krämer A, Michel J, Mitchell JA, Pande VS, Rodrigues JP, ... ... Chodera JD, et al. OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials. Arxiv. PMID 37986730  0.495
2023 Boby ML, Fearon D, Ferla M, Filep M, Koekemoer L, Robinson MC, Chodera JD, Lee AA, London N, von Delft A, von Delft F, Achdout H, Aimon A, Alonzi DS, Arbon R, et al. Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors. Science (New York, N.Y.). 382: eabo7201. PMID 37943932 DOI: 10.1126/science.abo7201  0.772
2023 Zhang I, Rufa DA, Pulido I, Henry MM, Rosen LE, Hauser K, Singh S, Chodera JD. Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex. Journal of Chemical Theory and Computation. PMID 37450482 DOI: 10.1021/acs.jctc.3c00333  0.473
2023 Boothroyd S, Behara PK, Madin OC, Hahn DF, Jang H, Gapsys V, Wagner JR, Horton JT, Dotson DL, Thompson MW, Maat J, Gokey T, Wang LP, Cole DJ, Gilson MK, ... Chodera JD, et al. Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. Journal of Chemical Theory and Computation. PMID 37167319 DOI: 10.1021/acs.jctc.3c00039  0.787
2023 Zhang I, Rufa DA, Pulido I, Henry MM, Rosen LE, Hauser K, Singh S, Chodera JD. Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex. Biorxiv : the Preprint Server For Biology. PMID 36945557 DOI: 10.1101/2023.03.07.530278  0.474
2023 Perner F, Stein EM, Wenge DV, Singh S, Kim J, Apazidis A, Rahnamoun H, Anand D, Marinaccio C, Hatton C, Wen Y, Stone RM, Schaller D, Mowla S, Xiao W, ... ... Chodera JD, et al. MEN1 mutations mediate clinical resistance to menin inhibition. Nature. PMID 36922589 DOI: 10.1038/s41586-023-05755-9  0.374
2023 Outhwaite IR, Singh S, Berger BT, Knapp S, Chodera JD, Seeliger MA. Death by a Thousand Cuts â€" Combining Kinase Inhibitors for Selective Target Inhibition and Rational Polypharmacology. Biorxiv : the Preprint Server For Biology. PMID 36711619 DOI: 10.1101/2023.01.13.523972  0.642
2022 Hahn DF, Bayly CI, Macdonald HEB, Chodera JD, Mey ASJS, Mobley DL, Benito LP, Schindler CEM, Tresadern G, Warren GL. Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1]. Living Journal of Computational Molecular Science. 4. PMID 36382113 DOI: 10.33011/livecoms.4.1.1497  0.594
2022 Horton JT, Boothroyd S, Wagner J, Mitchell JA, Gokey T, Dotson DL, Behara PK, Ramaswamy VK, Mackey M, Chodera JD, Anwar J, Mobley DL, Cole DJ. Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale. Journal of Chemical Information and Modeling. PMID 36351167 DOI: 10.1021/acs.jcim.2c01153  0.587
2022 Ackloo S, Al-Awar R, Amaro RE, Arrowsmith CH, Azevedo H, Batey RA, Bengio Y, Betz UAK, Bologa CG, Chodera JD, Cornell WD, Dunham I, Ecker GF, Edfeldt K, Edwards AM, et al. CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding. Nature Reviews. Chemistry. 6: 287-295. PMID 35783295 DOI: 10.1038/s41570-022-00363-z  0.532
2022 Boothroyd S, Madin OC, Mobley DL, Wang LP, Chodera JD, Shirts MR. Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties. Journal of Chemical Theory and Computation. PMID 35533269 DOI: 10.1021/acs.jctc.1c01268  0.784
2022 Boothroyd S, Wang LP, Mobley DL, Chodera JD, Shirts MR. Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation. Journal of Chemical Theory and Computation. PMID 35507313 DOI: 10.1021/acs.jctc.1c01111  0.791
2022 Grosjean H, Işık M, Aimon A, Mobley D, Chodera J, von Delft F, Biggin PC. SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction. Journal of Computer-Aided Molecular Design. PMID 35426591 DOI: 10.1007/s10822-022-00452-7  0.583
2022 Madin OC, Boothroyd S, Messerly RA, Fass J, Chodera JD, Shirts MR. Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models. Journal of Chemical Information and Modeling. 62: 874-889. PMID 35129974 DOI: 10.1021/acs.jcim.1c00829  0.584
2021 Smith DGA, Lolinco AT, Glick ZL, Lee J, Alenaizan A, Barnes TA, Borca CH, Di Remigio R, Dotson DL, Ehlert S, Heide AG, Herbst MF, Hermann J, Hicks CB, Horton JT, ... ... Chodera JD, et al. Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs. The Journal of Chemical Physics. 155: 204801. PMID 34852489 DOI: 10.1063/5.0059356  0.584
2021 Lyczek A, Berger BT, Rangwala AM, Paung Y, Tom J, Philipose H, Guo J, Albanese SK, Robers MB, Knapp S, Chodera JD, Seeliger MA. Mutation in Abl kinase with altered drug-binding kinetics indicates a novel mechanism of imatinib resistance. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34750265 DOI: 10.1073/pnas.2111451118  0.581
2021 Bahr MN, Nandkeolyar A, Kenna JK, Nevins N, Da Vià L, Işık M, Chodera JD, Mobley DL. Automated high throughput pK and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge. Journal of Computer-Aided Molecular Design. 35: 1141-1155. PMID 34714468 DOI: 10.1007/s10822-021-00427-0  0.598
2021 Qiu Y, Smith DGA, Boothroyd S, Jang H, Hahn DF, Wagner J, Bannan CC, Gokey T, Lim VT, Stern CD, Rizzi A, Tjanaka B, Tresadern G, Lucas X, Shirts MR, ... ... Chodera JD, et al. Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. Journal of Chemical Theory and Computation. PMID 34551262 DOI: 10.1021/acs.jctc.1c00571  0.789
2021 Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, ... ... Chodera JD, et al. SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome. Nature Chemistry. PMID 34031561 DOI: 10.1038/s41557-021-00707-0  0.764
2021 Işık M, Rustenburg AS, Rizzi A, Gunner MR, Mobley DL, Chodera JD. Overview of the SAMPL6 pK challenge: evaluating small molecule microscopic and macroscopic pK predictions. Journal of Computer-Aided Molecular Design. PMID 33394238 DOI: 10.1007/s10822-020-00362-6  0.572
2020 Mey ASJS, Allen BK, Macdonald HEB, Chodera JD, Hahn DF, Kuhn M, Michel J, Mobley DL, Naden LN, Prasad S, Rizzi A, Scheen J, Shirts MR, Tresadern G, Xu H. Best Practices for Alchemical Free Energy Calculations [Article v1.0]. Living Journal of Computational Molecular Science. 2. PMID 34458687 DOI: 10.33011/livecoms.2.1.18378  0.734
2020 Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, ... ... Chodera JD, et al. Citizen Scientists Create an Exascale Computer to Combat COVID-19. Biorxiv : the Preprint Server For Biology. PMID 32637963 DOI: 10.1101/2020.06.27.175430  0.761
2020 Gkeka P, Stoltz G, Barati Farimani A, Belkacemi Z, Ceriotti M, Chodera JD, Dinner AR, Ferguson AL, Maillet JB, Minoux H, Peter C, Pietrucci F, Silveira A, Tkatchenko A, Trstanova Z, et al. Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems. Journal of Chemical Theory and Computation. PMID 32559068 DOI: 10.1021/Acs.Jctc.0C00355  0.352
2020 Işık M, Bergazin TD, Fox T, Rizzi A, Chodera JD, Mobley DL. Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge. Journal of Computer-Aided Molecular Design. PMID 32107702 DOI: 10.1007/S10822-020-00295-0  0.597
2020 Gunner MR, Murakami T, Rustenburg AS, Işık M, Chodera JD. Standard state free energies, not pKs, are ideal for describing small molecule protonation and tautomeric states. Journal of Computer-Aided Molecular Design. PMID 32052350 DOI: 10.1007/S10822-020-00280-7  0.313
2020 Rizzi A, Jensen T, Slochower DR, Aldeghi M, Gapsys V, Ntekoumes D, Bosisio S, Papadourakis M, Henriksen NM, de Groot BL, Cournia Z, Dickson A, Michel J, Gilson MK, Shirts MR, ... ... Chodera JD, et al. The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations. Journal of Computer-Aided Molecular Design. PMID 31984465 DOI: 10.1007/S10822-020-00290-5  0.771
2019 Işık M, Levorse D, Mobley DL, Rhodes T, Chodera JD. Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge. Journal of Computer-Aided Molecular Design. PMID 31858363 DOI: 10.1007/S10822-019-00271-3  0.605
2019 Slochower DR, Henriksen NM, Wang LP, Chodera JD, Mobley DL, Gilson M. Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative. Journal of Chemical Theory and Computation. PMID 31603667 DOI: 10.1021/Acs.Jctc.9B00748  0.761
2019 Abraham MJ, Apostolov RP, Barnoud J, Bauer P, Blau C, Bonvin AMJJ, Chavent M, Chodera JD, Čondić-Jurkić K, Delemotte L, Grubmüller H, Howard RJ, Jordan EJ, Lindal E, Ollila OHS, et al. Sharing Data from Molecular Simulations. Journal of Chemical Information and Modeling. PMID 31525920 DOI: 10.1021/Acs.Jcim.9B00665  0.392
2019 Chen S, Wiewiora RP, Meng F, Babault N, Ma A, Yu W, Qian K, Hu H, Zou H, Wang J, Fan S, Blum G, Pittella-Silva F, Beauchamp KA, Tempel W, ... ... Chodera JD, et al. The dynamic conformational landscape of the protein methyltransferase SETD8. Elife. 8. PMID 31081496 DOI: 10.7554/Elife.45403  0.399
2019 Wiewiora RP, Chen S, Luo M, Chodera JD. Markov Models of Functional Dynamics of Histone Lysine Methyltransferases by Millisecond-Timescale Molecular Simulation and Chemical Probing Biophysical Journal. 116: 183a. DOI: 10.1016/J.Bpj.2018.11.1016  0.346
2018 Hanson SM, Georghiou G, Thakur MK, Miller WT, Rest JS, Chodera JD, Seeliger MA. What Makes a Kinase Promiscuous for Inhibitors? Cell Chemical Biology. PMID 30612951 DOI: 10.1016/J.Chembiol.2018.11.005  0.631
2018 Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL. Toward learned chemical perception of force field typing rules. Journal of Chemical Theory and Computation. PMID 30512951 DOI: 10.1021/Acs.Jctc.8B00821  0.727
2018 Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD. Overview of the SAMPL6 host-guest binding affinity prediction challenge. Journal of Computer-Aided Molecular Design. PMID 30415285 DOI: 10.1007/S10822-018-0170-6  0.64
2018 Işık M, Levorse D, Rustenburg AS, Ndukwe IE, Wang H, Wang X, Reibarkh M, Martin GE, Makarov AA, Mobley DL, Rhodes T, Chodera JD. pK measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments. Journal of Computer-Aided Molecular Design. PMID 30406372 DOI: 10.1007/S10822-018-0168-0  0.62
2018 Fass J, Sivak DA, Crooks GE, Beauchamp KA, Leimkuhler B, Chodera JD. Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems. Entropy (Basel, Switzerland). 20. PMID 30393452 DOI: 10.3390/E20050318  0.664
2018 Swenson D, Prinz JH, Noé F, Chodera JD, Bolhuis PG. OpenPathSampling: A Python framework for path sampling simulations. II. Building and customizing path ensembles and sample schemes. Journal of Chemical Theory and Computation. PMID 30359525 DOI: 10.1021/Acs.Jctc.8B00627  0.331
2018 Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Eastman PK. Escaping atom types in force fields using direct chemical perception. Journal of Chemical Theory and Computation. PMID 30351006 DOI: 10.1021/Acs.Jctc.8B00640  0.715
2018 Swenson D, Prinz JH, Noé F, Chodera JD, Bolhuis PG. OpenPathSampling: A Python framework for path sampling simulations. I. Basics. Journal of Chemical Theory and Computation. PMID 30336030 DOI: 10.1021/Acs.Jctc.8B00626  0.362
2018 Nguyen TH, Rustenburg AS, Krimmer SG, Zhang H, Clark JD, Novick PA, Branson K, Pande VS, Chodera JD, Minh DDL. Bayesian analysis of isothermal titration calorimetry for binding thermodynamics. Plos One. 13: e0203224. PMID 30212471 DOI: 10.1371/Journal.Pone.0203224  0.535
2018 Albanese SK, Parton DL, Isik M, Rodríguez-Laureano L, Hanson SM, Behr JM, Gradia S, Jeans C, Levinson NM, Seeliger MA, Chodera JD. An open library of human kinase domain constructs for automated bacterial expression. Biochemistry. PMID 30004690 DOI: 10.1021/Acs.Biochem.7B01081  0.618
2018 Ross GA, Rustenburg AS, Grinaway PB, Fass J, Chodera JD. Biomolecular Simulations Under Realistic Macroscopic Salt Conditions. The Journal of Physical Chemistry. B. PMID 29649876 DOI: 10.1021/Acs.Jpcb.7B11734  0.362
2018 Amaro RE, Baudry J, Chodera J, Demir Ö, McCammon JA, Miao Y, Smith JC. Ensemble Docking in Drug Discovery. Biophysical Journal. PMID 29606412 DOI: 10.1016/J.Bpj.2018.02.038  0.639
2018 Gill SC, Lim NM, Grinaway PB, Rustenburg AS, Fass J, Ross GA, Chodera JD, Mobley DL. Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo. The Journal of Physical Chemistry. B. PMID 29486559 DOI: 10.1021/Acs.Jpcb.7B11820  0.606
2018 Wiewiora RP, Chen S, Luo M, Chodera JD. Conformational Dynamics of Histone Methyltransferase SET8 Probed by Millisecond-Timescale Molecular Dynamics, Markov State Modeling and Biochemical Experiments Biophysical Journal. 114: 398a. DOI: 10.1016/J.Bpj.2017.11.2203  0.322
2017 Matos GDR, Kyu DY, Loeffler HH, Chodera JD, Shirts MR, Mobley DL. Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database. Journal of Chemical and Engineering Data. 62: 1559-1569. PMID 29056756 DOI: 10.1021/Acs.Jced.7B00104  0.749
2017 Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. Plos Computational Biology. 13: e1005659. PMID 28746339 DOI: 10.1371/Journal.Pcbi.1005659  0.758
2017 Hanson SM, Fass JH, Chodera JD. Can we Automatically Detect Biologically Relevant Order Parameters in Molecular Simulation? Comparing Long Timescale Simulations of Multiple Kinases Biophysical Journal. 112: 32a. DOI: 10.1016/J.Bpj.2016.11.208  0.395
2017 Wiewiora RP, Chen S, Beauchamp K, Luo M, Chodera JD. Conformational Dynamics of Histone Lysine Methyltransferases by Millisecond-Timescale Molecular Dynamics on Folding@home Biophysical Journal. 112: 189a. DOI: 10.1016/J.Bpj.2016.11.1048  0.303
2016 Rustenburg AS, Dancer J, Lin B, Feng JA, Ortwine DF, Mobley DL, Chodera JD. Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge. Journal of Computer-Aided Molecular Design. PMID 27718028 DOI: 10.1007/S10822-016-9971-7  0.598
2016 Parton DL, Grinaway PB, Hanson SM, Beauchamp KA, Chodera JD. Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale. Plos Computational Biology. 12: e1004728. PMID 27337644 DOI: 10.1371/Journal.Pcbi.1004728  0.433
2016 Chodera JD. A Simple Method for Automated Equilibration Detection in Molecular Simulations. Journal of Chemical Theory and Computation. PMID 26771390 DOI: 10.1021/Acs.Jctc.5B00784  0.396
2016 Hanson SM, Rodriguez L, Behr JM, Rizzi A, Parton DL, Beauchamp KA, Fass JH, Prinz J, Boyce SE, Seeliger MA, Levinson NM, Chodera JD. Dissecting the Contribution of Kinase Conformational Reorganization Energies to Inhibitor Selectivity Biophysical Journal. 110: 545a. DOI: 10.1016/J.Bpj.2015.11.2918  0.68
2016 Stern CD, Perez-Aguilar JM, Blanchard SC, Weinstein H, Chodera JD. Bridging the Gap between Computation and Experiments in GPCRs Biophysical Journal. 110: 324a-325a. DOI: 10.1016/J.Bpj.2015.11.1743  0.392
2016 Albanese S, Xu J, Hsieh J, Chodera JD. Simulating mTOR Hyperactivating Mutations to Understand Functionally Significant Structural Rearrangements Biophysical Journal. 110: 207a. DOI: 10.1016/J.Bpj.2015.11.1152  0.33
2015 Hanson SM, Ekins S, Chodera JD. Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies. Journal of Computer-Aided Molecular Design. PMID 26678597 DOI: 10.1007/S10822-015-9888-6  0.303
2015 Beauchamp KA, Behr JM, Rustenburg AS, Bayly CI, Kroenlein K, Chodera JD. Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive. The Journal of Physical Chemistry. B. 119: 12912-20. PMID 26339862 DOI: 10.1021/Acs.Jpcb.5B06703  0.384
2015 Hanson SM, Prinz J, Behr JM, Grinaway PB, Rustenburg AS, Beauchamp KA, Parton DL, Chodera JD. Developing High-Throughput Fluorescence-Based Assays for Measuring Kinase Inhibitor Free Energies of Binding Biophysical Journal. 108: 357a. DOI: 10.1016/J.Bpj.2014.11.1958  0.333
2015 Beauchamp KA, Behr JM, Grinaway PB, Rustenburg AS, Chodera JD. Benchmarking and Optimizing Atomistic Forcefields with Density Measurements Biophysical Journal. 108: 182a-183a. DOI: 10.1016/J.Bpj.2014.11.1009  0.364
2014 Prinz JH, Chodera JD, Noé F. Spectral Rate Theory for Two-State Kinetics. Physical Review. X. 4. PMID 25356374 DOI: 10.1103/Physrevx.4.011020  0.331
2014 Chodera JD, Noé F. Markov state models of biomolecular conformational dynamics. Current Opinion in Structural Biology. 25: 135-44. PMID 24836551 DOI: 10.1016/J.Sbi.2014.04.002  0.429
2014 Sivak DA, Chodera JD, Crooks GE. Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems. The Journal of Physical Chemistry. B. 118: 6466-74. PMID 24555448 DOI: 10.1021/Jp411770F  0.655
2014 Prinz JH, Chodera JD, Noé F. Estimation and validation of Markov models. Advances in Experimental Medicine and Biology. 797: 45-60. PMID 24297274 DOI: 10.1007/978-94-007-7606-7_4  0.33
2014 Sivak DA, Chodera JD, Crooks GE. Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems Journal of Physical Chemistry B. 118: 6466-6474. DOI: 10.1021/jp411770f  0.588
2014 Parton DL, Shukla D, Zhao Y, Pande VS, Chodera JD. Toward a Global View of the Conformational Landscape of the Human Kinome Biophysical Journal. 106: 655a-656a. DOI: 10.1016/J.Bpj.2013.11.3628  0.702
2014 Wang L, Head-Gordon T, Ponder J, Ren P, Chodera J, Eastman P, Martinez TJ, Pande VS. Systematic Improvement on the Classical Molecular Model of Water Biophysical Journal. 106: 403a. DOI: 10.1016/J.Bpj.2013.11.2273  0.696
2014 Sivak DA, Chodera JD, Crooks GE. Numerical Langevin Simulations: Equilibrium Dynamics and Nonequilibrium Thermodynamics Biophysical Journal. 106: 403a. DOI: 10.1016/J.Bpj.2013.11.2269  0.684
2013 Wang K, Chodera JD, Yang Y, Shirts MR. Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. Journal of Computer-Aided Molecular Design. 27: 989-1007. PMID 24297454 DOI: 10.1007/S10822-013-9689-8  0.645
2013 Wang LP, Head-Gordon T, Ponder JW, Ren P, Chodera JD, Eastman PK, Martinez TJ, Pande VS. Systematic improvement of a classical molecular model of water. The Journal of Physical Chemistry. B. 117: 9956-72. PMID 23750713 DOI: 10.1021/Jp403802C  0.697
2013 Chodera JD, Mobley DL. Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design. Annual Review of Biophysics. 42: 121-42. PMID 23654303 DOI: 10.1146/Annurev-Biophys-083012-130318  0.605
2013 Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang LP, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts MR, et al. OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. Journal of Chemical Theory and Computation. 9: 461-469. PMID 23316124 DOI: 10.1021/Ct300857J  0.783
2013 Sivak DA, Chodera JD, Crooks GE. Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium simulations of discrete Langevin dynamics Physical Review X. 3. DOI: 10.1103/Physrevx.3.011007  0.671
2013 Eastman P, Friedrichs MS, Chodera JD, Radmer RJ, Bruns CM, Ku JP, Beauchamp KA, Lane TJ, Wang LP, Shukla D, Tye T, Houston M, Stich T, Klein C, Shirts MR, et al. OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation Journal of Chemical Theory and Computation. 9: 461-469. DOI: 10.1021/ct300857j  0.786
2013 Wang K, Yang Y, Chodera JD, Shirts MR. Identifying ligand binding sites and poses using Hamiltonian replica exchange molecular dynamics: Model systems and a validation study using the astex diverse set Engineering Sciences and Fundamentals 2013 - Core Programming Area At the 2013 Aiche Annual Meeting: Global Challenges For Engineering a Sustainable Future. 2: 622.  0.591
2012 Pitera JW, Chodera JD. On the Use of Experimental Observations to Bias Simulated Ensembles. Journal of Chemical Theory and Computation. 8: 3445-51. PMID 26592995 DOI: 10.1021/Ct300112V  0.348
2012 Elms PJ, Chodera JD, Bustamante CJ, Marqusee S. Limitations of constant-force-feedback experiments. Biophysical Journal. 103: 1490-9. PMID 23062341 DOI: 10.1016/J.Bpj.2012.06.051  0.35
2012 Elms PJ, Chodera JD, Bustamante C, Marqusee S. The molten globule state is unusually deformable under mechanical force. Proceedings of the National Academy of Sciences of the United States of America. 109: 3796-801. PMID 22355138 DOI: 10.1073/Pnas.1115519109  0.304
2012 Chodera JD, Pande VS. Erratum: Splitting Probabilities as a Test of Reaction Coordinate Choice in Single-Molecule Experiments [Phys. Rev. Lett.107, 098102 (2011)] Physical Review Letters. 108. DOI: 10.1103/Physrevlett.108.249901  0.469
2012 Minh DDL, Chodera JD. 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)] The Journal of Chemical Physics. 136: 029901. DOI: 10.1063/1.3673567  0.33
2011 Chodera JD, Shirts MR. Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing. The Journal of Chemical Physics. 135: 194110. PMID 22112069 DOI: 10.1063/1.3660669  0.655
2011 Nilmeier JP, Crooks GE, Minh DD, Chodera JD. Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation. Proceedings of the National Academy of Sciences of the United States of America. 108: E1009-18. PMID 22025687 DOI: 10.1073/Pnas.1106094108  0.426
2011 Chodera JD, Pande VS. Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments. Physical Review Letters. 107: 098102. PMID 21929272 DOI: 10.1103/Physrevlett.107.098102  0.501
2011 Chodera JD, Pande VS. The social network (of protein conformations). Proceedings of the National Academy of Sciences of the United States of America. 108: 12969-70. PMID 21804033 DOI: 10.1073/Pnas.1109571108  0.439
2011 Prinz JH, Chodera JD, Pande VS, Swope WC, Smith JC, Noé F. Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. The Journal of Chemical Physics. 134: 244108. PMID 21721613 DOI: 10.1063/1.3592153  0.71
2011 Chodera JD, Swope WC, Noé F, Prinz JH, Shirts MR, Pande VS. Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. The Journal of Chemical Physics. 134: 244107. PMID 21721612 DOI: 10.1063/1.3592152  0.783
2011 Prinz JH, Wu H, Sarich M, Keller B, Senne M, Held M, Chodera JD, Schütte C, Noé F. Markov models of molecular kinetics: generation and validation. The Journal of Chemical Physics. 134: 174105. PMID 21548671 DOI: 10.1063/1.3565032  0.394
2011 Noé F, Doose S, Daidone I, Löllmann M, Sauer M, Chodera JD, Smith JC. Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments. Proceedings of the National Academy of Sciences of the United States of America. 108: 4822-7. PMID 21368203 DOI: 10.1073/Pnas.1004646108  0.38
2011 Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS. Alchemical free energy methods for drug discovery: progress and challenges. Current Opinion in Structural Biology. 21: 150-60. PMID 21349700 DOI: 10.1016/J.Sbi.2011.01.011  0.757
2011 Minh DD, Chodera JD. 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. The Journal of Chemical Physics. 134: 024111. PMID 21241084 DOI: 10.1063/1.3516517  0.364
2011 Chodera JD, Pande VS. Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments Physical Review Letters. 107. DOI: 10.1103/PhysRevLett.107.098102  0.394
2011 Chodera JD, Pande VS. The social network (of protein conformations) Proceedings of the National Academy of Sciences of the United States of America. 108: 12969-12970. DOI: 10.1073/pnas.1109571108  0.375
2010 Chodera JD, Noé F. Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolution. The Journal of Chemical Physics. 133: 105102. PMID 20849191 DOI: 10.1063/1.3463406  0.378
2010 Adelman JL, Chodera JD, Kuo IF, Miller TF, Barsky D. The mechanical properties of PCNA: implications for the loading and function of a DNA sliding clamp. Biophysical Journal. 98: 3062-9. PMID 20550919 DOI: 10.1016/J.Bpj.2010.03.056  0.305
2010 Ponder JW, Wu C, Ren P, Pande VS, Chodera JD, Schnieders MJ, Haque I, Mobley DL, Lambrecht DS, DiStasio RA, Head-Gordon M, Clark GN, Johnson ME, Head-Gordon T. Current status of the AMOEBA polarizable force field. The Journal of Physical Chemistry. B. 114: 2549-64. PMID 20136072 DOI: 10.1021/Jp910674D  0.724
2009 Minh DD, Chodera JD. Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages. The Journal of Chemical Physics. 131: 134110. PMID 19814546 DOI: 10.1063/1.3242285  0.321
2009 Bacallado S, Chodera JD, Pande V. Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint. The Journal of Chemical Physics. 131: 045106. PMID 19655927 DOI: 10.1063/1.3192309  0.567
2008 Shirts MR, Chodera JD. Statistically optimal analysis of samples from multiple equilibrium states. The Journal of Chemical Physics. 129: 124105. PMID 19045004 DOI: 10.1063/1.2978177  0.628
2008 Nicholls A, Mobley DL, Guthrie JP, Chodera JD, Bayly CI, Cooper MD, Pande VS. Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. Journal of Medicinal Chemistry. 51: 769-79. PMID 18215013 DOI: 10.1021/Jm070549+  0.704
2008 Mobley DL, Dill KA, Chodera JD. Treating entropy and conformational changes in implicit solvent simulations of small molecules. The Journal of Physical Chemistry. B. 112: 938-46. PMID 18171044 DOI: 10.1021/Jp0764384  0.695
2008 Shirts MR, Chodera JD. Statistically optimal free energy estimates from sparsely chosen states Aiche Annual Meeting, Conference Proceedings.  0.562
2007 Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA. Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations. Journal of Chemical Theory and Computation. 3: 26-41. PMID 26627148 DOI: 10.1021/Ct0502864  0.789
2007 Mobley DL, Chodera JD, Dill KA. The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. Journal of Chemical Theory and Computation. 3: 1231-1235. PMID 18843379 DOI: 10.1021/Ct700032N  0.7
2007 Shirts MR, Mobley DL, Chodera JD, Pande VS. Accurate and efficient corrections for missing dispersion interactions in molecular simulations. The Journal of Physical Chemistry. B. 111: 13052-63. PMID 17949030 DOI: 10.1021/Jp0735987  0.793
2007 Ozkan SB, Wu GA, Chodera JD, Dill KA. Protein folding by zipping and assembly. Proceedings of the National Academy of Sciences of the United States of America. 104: 11987-92. PMID 17620603 DOI: 10.1073/Pnas.0703700104  0.724
2007 Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA. Predicting absolute ligand binding free energies to a simple model site. Journal of Molecular Biology. 371: 1118-34. PMID 17599350 DOI: 10.1016/J.Jmb.2007.06.002  0.699
2007 Dill KA, Ozkan SB, Weikl TR, Chodera JD, Voelz VA. The protein folding problem: when will it be solved? Current Opinion in Structural Biology. 17: 342-6. PMID 17572080 DOI: 10.1016/J.Sbi.2007.06.001  0.771
2007 Chodera JD, Singhal N, Pande VS, Dill KA, Swope WC. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. The Journal of Chemical Physics. 126: 155101. PMID 17461665 DOI: 10.1063/1.2714538  0.749
2007 Mobley DL, Dumont E, Chodera JD, Dill KA. Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. The Journal of Physical Chemistry. B. 111: 2242-54. PMID 17291029 DOI: 10.1021/Jp0667442  0.699
2007 Chodera JD, Swope WC, Pitera JW, Seok C, Dill KA. Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations Journal of Chemical Theory and Computation. 3: 26-41. DOI: 10.1021/ct0502864  0.68
2007 Shirts MR, Mobley DL, Chodera JD. Chapter 4 Alchemical Free Energy Calculations: Ready for Prime Time? Annual Reports in Computational Chemistry. 3: 41-59. DOI: 10.1016/S1574-1400(07)03004-6  0.751
2006 Mobley DL, Chodera JD, Dill KA. On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. The Journal of Chemical Physics. 125: 084902. PMID 16965052 DOI: 10.1063/1.2221683  0.707
2006 Chodera JD, Swope WC, Pitera JW, Dill KA. Long-time protein folding dynamics from short-time molecular dynamics simulations Multiscale Modeling and Simulation. 5: 1214-1226. DOI: 10.1137/06065146X  0.715
2003 Seok C, Rosen JB, Chodera JD, Dill KA. MOPED: method for optimizing physical energy parameters using decoys. Journal of Computational Chemistry. 24: 89-97. PMID 12483678 DOI: 10.1002/Jcc.10124  0.69
2001 Lee TS, Chong LT, Chodera JD, Kollman PA. An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase. Journal of the American Chemical Society. 123: 12837-48. PMID 11749542 DOI: 10.1021/Ja011096F  0.679
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