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What Makes a Kinase Promiscuous for Inhibitors?

Hanson SM, Georghiou G, Thakur MK, Miller WT, Rest JS, Chodera JD, Seeliger MA.

Cell Chem Biol. 2018 Dec 11. pii: S2451-9456(18)30412-4. doi: 10.1016/j.chembiol.2018.11.005. [Epub ahead of print]


Toward learned chemical perception of force field typing rules.

Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL.

J Chem Theory Comput. 2018 Dec 4. doi: 10.1021/acs.jctc.8b00821. [Epub ahead of print]


Overview of the SAMPL6 host-guest binding affinity prediction challenge.

Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD.

J Comput Aided Mol Des. 2018 Oct;32(10):937-963. doi: 10.1007/s10822-018-0170-6. Epub 2018 Nov 10.


pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments.

Işık M, Levorse D, Rustenburg AS, Ndukwe IE, Wang H, Wang X, Reibarkh M, Martin GE, Makarov AA, Mobley DL, Rhodes T, Chodera JD.

J Comput Aided Mol Des. 2018 Oct;32(10):1117-1138. doi: 10.1007/s10822-018-0168-0. Epub 2018 Nov 7.


Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems.

Fass J, Sivak DA, Crooks GE, Beauchamp KA, Leimkuhler B, Chodera JD.

Entropy (Basel). 2018 May;20(5). pii: 318. doi: 10.3390/e20050318. Epub 2018 Apr 26.


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

Swenson D, Prinz JH, Noé F, Chodera JD, Bolhuis PG.

J Chem Theory Comput. 2018 Oct 25. doi: 10.1021/acs.jctc.8b00627. [Epub ahead of print]


Escaping Atom Types in Force Fields Using Direct Chemical Perception.

Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK.

J Chem Theory Comput. 2018 Nov 13;14(11):6076-6092. doi: 10.1021/acs.jctc.8b00640. Epub 2018 Oct 30.


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

Swenson D, Prinz JH, Noé F, Chodera JD, Bolhuis PG.

J Chem Theory Comput. 2018 Oct 18. doi: 10.1021/acs.jctc.8b00626. [Epub ahead of print]


Bayesian analysis of isothermal titration calorimetry for binding thermodynamics.

Nguyen TH, Rustenburg AS, Krimmer SG, Zhang H, Clark JD, Novick PA, Branson K, Pande VS, Chodera JD, Minh DDL.

PLoS One. 2018 Sep 13;13(9):e0203224. doi: 10.1371/journal.pone.0203224. eCollection 2018.


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

Hauser K, Negron C, Albanese SK, Ray S, Steinbrecher T, Abel R, Chodera JD, Wang L.

Commun Biol. 2018;1. pii: 70. doi: 10.1101/239012. Epub 2018 Jun 13.


An Open Library of Human Kinase Domain Constructs for Automated Bacterial Expression.

Albanese SK, Parton DL, Işık M, Rodríguez-Laureano L, Hanson SM, Behr JM, Gradia S, Jeans C, Levinson NM, Seeliger MA, Chodera JD.

Biochemistry. 2018 Aug 7;57(31):4675-4689. doi: 10.1021/acs.biochem.7b01081. Epub 2018 Jul 26.


Acquired resistance to IDH inhibition through trans or cis dimer-interface mutations.

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, Cross JR, Tallman MS, Arcila ME, Roshal M, Petsko GA, Wu B, Choe S, Konteatis ZD, Biller SA, Chodera JD, Thompson CB, Levine RL, Stein EM.

Nature. 2018 Jul;559(7712):125-129. doi: 10.1038/s41586-018-0251-7. Epub 2018 Jun 27.


Biomolecular Simulations under Realistic Macroscopic Salt Conditions.

Ross GA, Rustenburg AS, Grinaway PB, Fass J, Chodera JD.

J Phys Chem B. 2018 May 31;122(21):5466-5486. doi: 10.1021/acs.jpcb.7b11734.


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

Gill SC, Lim NM, Grinaway PB, Rustenburg AS, Fass J, Ross GA, Chodera JD, Mobley DL.

J Phys Chem B. 2018 May 31;122(21):5579-5598. doi: 10.1021/acs.jpcb.7b11820. Epub 2018 Mar 12.


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

Ruff EF, Muretta JM, Thompson AR, Lake EW, Cyphers S, Albanese SK, Hanson SM, Behr JM, Thomas DD, Chodera JD, Levinson NM.

Elife. 2018 Feb 21;7. pii: e32766. doi: 10.7554/eLife.32766.


Quantitative self-assembly prediction yields targeted nanomedicines.

Shamay Y, Shah J, Işık M, Mizrachi A, Leibold J, Tschaharganeh DF, Roxbury D, Budhathoki-Uprety J, Nawaly K, Sugarman JL, Baut E, Neiman MR, Dacek M, Ganesh KS, Johnson DC, Sridharan R, Chu KL, Rajasekhar VK, Lowe SW, Chodera JD, Heller DA.

Nat Mater. 2018 Apr;17(4):361-368. doi: 10.1038/s41563-017-0007-z. Epub 2018 Feb 5.


Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database.

Matos GDR, Kyu DY, Loeffler HH, Chodera JD, Shirts MR, Mobley DL.

J Chem Eng Data. 2017 May 11;62(5):1559-1569. doi: 10.1021/acs.jced.7b00104. Epub 2017 Apr 24.


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

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.

PLoS Comput Biol. 2017 Jul 26;13(7):e1005659. doi: 10.1371/journal.pcbi.1005659. eCollection 2017 Jul.


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

Intlekofer AM, Wang B, Liu H, Shah H, Carmona-Fontaine C, Rustenburg AS, Salah S, Gunner MR, Chodera JD, Cross JR, Thompson CB.

Nat Chem Biol. 2017 May;13(5):494-500. doi: 10.1038/nchembio.2307. Epub 2017 Mar 6.


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

Cyphers S, Ruff EF, Behr JM, Chodera JD, Levinson NM.

Nat Chem Biol. 2017 Apr;13(4):402-408. doi: 10.1038/nchembio.2296. Epub 2017 Feb 6.


Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge.

Rustenburg AS, Dancer J, Lin B, Feng JA, Ortwine DF, Mobley DL, Chodera JD.

J Comput Aided Mol Des. 2016 Nov;30(11):945-958. doi: 10.1007/s10822-016-9971-7. Epub 2016 Oct 7.


Mechanistically distinct cancer-associated mTOR activation clusters predict sensitivity to rapamycin.

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.

J Clin Invest. 2016 Sep 1;126(9):3526-40. doi: 10.1172/JCI86120. Epub 2016 Aug 2.


Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale.

Parton DL, Grinaway PB, Hanson SM, Beauchamp KA, Chodera JD.

PLoS Comput Biol. 2016 Jun 23;12(6):e1004728. doi: 10.1371/journal.pcbi.1004728. eCollection 2016 Jun.


A Simple Method for Automated Equilibration Detection in Molecular Simulations.

Chodera JD.

J Chem Theory Comput. 2016 Apr 12;12(4):1799-805. doi: 10.1021/acs.jctc.5b00784. Epub 2016 Mar 23.


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

Hanson SM, Ekins S, Chodera JD.

J Comput Aided Mol Des. 2015 Dec;29(12):1073-86. doi: 10.1007/s10822-015-9888-6. Epub 2015 Dec 17.


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

Beauchamp KA, Behr JM, Rustenburg AS, Bayly CI, Kroenlein K, Chodera JD.

J Phys Chem B. 2015 Oct 8;119(40):12912-20. doi: 10.1021/acs.jpcb.5b06703. Epub 2015 Sep 29.


Hypoxia Induces Production of L-2-Hydroxyglutarate.

Intlekofer AM, Dematteo RG, Venneti S, Finley LW, Lu C, Judkins AR, Rustenburg AS, Grinaway PB, Chodera JD, Cross JR, Thompson CB.

Cell Metab. 2015 Aug 4;22(2):304-11. doi: 10.1016/j.cmet.2015.06.023. Epub 2015 Jul 23.


Spectral Rate Theory for Two-State Kinetics.

Prinz JH, Chodera JD, Noé F.

Phys Rev X. 2014 Feb;4(1). pii: 011020.


Markov state models of biomolecular conformational dynamics.

Chodera JD, Noé F.

Curr Opin Struct Biol. 2014 Apr;25:135-44. doi: 10.1016/ Epub 2014 May 16. Review.


Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems.

Sivak DA, Chodera JD, Crooks GE.

J Phys Chem B. 2014 Jun 19;118(24):6466-74. doi: 10.1021/jp411770f. Epub 2014 Mar 17.


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

Wang K, Chodera JD, Yang Y, Shirts MR.

J Comput Aided Mol Des. 2013 Dec;27(12):989-1007. doi: 10.1007/s10822-013-9689-8. Epub 2013 Dec 3.


Uncertainty estimation.

Noé F, Chodera JD.

Adv Exp Med Biol. 2014;797:61-74. doi: 10.1007/978-94-007-7606-7_5. No abstract available.


Estimation and validation of Markov models.

Prinz JH, Chodera JD, Noé F.

Adv Exp Med Biol. 2014;797:45-60. doi: 10.1007/978-94-007-7606-7_4. Review. No abstract available.


Systematic improvement of a classical molecular model of water.

Wang LP, Head-Gordon T, Ponder JW, Ren P, Chodera JD, Eastman PK, Martinez TJ, Pande VS.

J Phys Chem B. 2013 Aug 29;117(34):9956-72. doi: 10.1021/jp403802c. Epub 2013 Aug 14.


Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design.

Chodera JD, Mobley DL.

Annu Rev Biophys. 2013;42:121-42. doi: 10.1146/annurev-biophys-083012-130318. Review.


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

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, Pande VS.

J Chem Theory Comput. 2013 Jan 8;9(1):461-469. Epub 2012 Oct 18.


Limitations of constant-force-feedback experiments.

Elms PJ, Chodera JD, Bustamante CJ, Marqusee S.

Biophys J. 2012 Oct 3;103(7):1490-9. doi: 10.1016/j.bpj.2012.06.051. Epub 2012 Oct 2.


On the Use of Experimental Observations to Bias Simulated Ensembles.

Pitera JW, Chodera JD.

J Chem Theory Comput. 2012 Oct 9;8(10):3445-51. doi: 10.1021/ct300112v. Epub 2012 Aug 27.


The molten globule state is unusually deformable under mechanical force.

Elms PJ, Chodera JD, Bustamante C, Marqusee S.

Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3796-801. doi: 10.1073/pnas.1115519109. Epub 2012 Feb 21.


The ribosome modulates nascent protein folding.

Kaiser CM, Goldman DH, Chodera JD, Tinoco I Jr, Bustamante C.

Science. 2011 Dec 23;334(6063):1723-7. doi: 10.1126/science.1209740.


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

Chodera JD, Shirts MR.

J Chem Phys. 2011 Nov 21;135(19):194110. doi: 10.1063/1.3660669.


Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation.

Nilmeier JP, Crooks GE, Minh DD, Chodera JD.

Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):E1009-18. doi: 10.1073/pnas.1106094108. Epub 2011 Oct 24. Erratum in: Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9665.


Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments.

Chodera JD, Pande VS.

Phys Rev Lett. 2011 Aug 26;107(9):098102. Epub 2011 Aug 23. Erratum in: Phys Rev Lett. 2012 Jun 15;108(24):249901.


The social network (of protein conformations).

Chodera JD, Pande VS.

Proc Natl Acad Sci U S A. 2011 Aug 9;108(32):12969-70. doi: 10.1073/pnas.1109571108. Epub 2011 Jul 29. No abstract available.


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

Prinz JH, Chodera JD, Pande VS, Swope WC, Smith JC, Noé F.

J Chem Phys. 2011 Jun 28;134(24):244108. doi: 10.1063/1.3592153.


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

Chodera JD, Swope WC, Noé F, Prinz JH, Shirts MR, Pande VS.

J Chem Phys. 2011 Jun 28;134(24):244107. doi: 10.1063/1.3592152.


Markov models of molecular kinetics: generation and validation.

Prinz JH, Wu H, Sarich M, Keller B, Senne M, Held M, Chodera JD, Schütte C, Noé F.

J Chem Phys. 2011 May 7;134(17):174105. doi: 10.1063/1.3565032.


Systematic errors in isothermal titration calorimetry: concentrations and baselines.

Tellinghuisen J, Chodera JD.

Anal Biochem. 2011 Jul 15;414(2):297-9. doi: 10.1016/j.ab.2011.03.024. Epub 2011 Mar 26.


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

Noé F, Doose S, Daidone I, Löllmann M, Sauer M, Chodera JD, Smith JC.

Proc Natl Acad Sci U S A. 2011 Mar 22;108(12):4822-7. doi: 10.1073/pnas.1004646108. Epub 2011 Mar 2.


Alchemical free energy methods for drug discovery: progress and challenges.

Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS.

Curr Opin Struct Biol. 2011 Apr;21(2):150-60. doi: 10.1016/ Epub 2011 Feb 23. Review.

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