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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 
 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

76 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, 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
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
2018 Intlekofer AM, Shih AH, Wang B, Nazir A, Rustenburg AS, Albanese SK, Patel M, Famulare C, Correa FM, Takemoto N, Durani V, Liu H, Taylor J, Farnoud N, Papaemmanuil E, ... ... Chodera JD, et al. Acquired resistance to IDH inhibition through trans or cis dimer-interface mutations. Nature. PMID 29950729 DOI: 10.1038/s41586-018-0251-7  1
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  1
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  1
2018 Ruff EF, Muretta JM, Thompson AR, Lake EW, Cyphers S, Albanese SK, Hanson SM, Behr JM, Thomas DD, Chodera JD, Levinson NM. A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation. Elife. 7. PMID 29465396 DOI: 10.7554/eLife.32766  1
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  1
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  1
2017 Intlekofer AM, Wang B, Liu H, Shah H, Carmona-Fontaine C, Rustenburg AS, Salah S, Gunner MR, Chodera JD, Cross JR, Thompson CB. L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH. Nature Chemical Biology. PMID 28263965 DOI: 10.1038/nchembio.2307  1
2017 Cyphers S, Ruff EF, Behr JM, Chodera JD, Levinson NM. A water-mediated allosteric network governs activation of Aurora kinase A. Nature Chemical Biology. PMID 28166210 DOI: 10.1038/nchembio.2296  1
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  1
2016 Xu J, Pham CG, Albanese SK, Dong Y, Oyama T, Lee CH, Rodrik-Outmezguine V, Yao Z, Han S, Chen D, Parton DL, Chodera JD, Rosen N, Cheng EH, Hsieh JJ. Mechanistically distinct cancer-associated mTOR activation clusters predict sensitivity to rapamycin. The Journal of Clinical Investigation. PMID 27482884 DOI: 10.1172/JCI86120  1
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  1
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  1
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  1
2015 Intlekofer AM, Dematteo RG, Venneti S, Finley LW, Lu C, Judkins AR, Rustenburg AS, Grinaway PB, Chodera JD, Cross JR, Thompson CB. Hypoxia Induces Production of L-2-Hydroxyglutarate. Cell Metabolism. PMID 26212717 DOI: 10.1016/j.cmet.2015.06.023  1
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  1
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  1
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  1
2014 Noé F, Chodera JD. Uncertainty estimation. Advances in Experimental Medicine and Biology. 797: 61-74. PMID 24297275 DOI: 10.1007/978-94-007-7606-7_5  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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.  1
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  1
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  1
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  1
2012 Nilmeier JP, Crooks GE, Minh DDL, 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 (2011) 108, 45 (E1009-E1018) 10.1073/pnas.1106094108) Proceedings of the National Academy of Sciences of the United States of America. 109: 9665. DOI: 10.1073/pnas.1207617109  1
2011 Kaiser CM, Goldman DH, Chodera JD, Tinoco I, Bustamante C. The ribosome modulates nascent protein folding. Science (New York, N.Y.). 334: 1723-7. PMID 22194581 DOI: 10.1126/science.1209740  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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+  1
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  1
2008 Shirts MR, Chodera JD. Statistically optimal free energy estimates from sparsely chosen states Aiche Annual Meeting, Conference Proceedings 1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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  1
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