publications
Publications in reversed chronological order by year. Current members and alumni are linked to their member page.
2026
- A computational community blind challenge on pan-coronavirus drug discovery data2026Github: https://github.com/asapdiscovery/asap-blind-challenge-paper
- Trastuzumab Deruxtecan Resistance via Loss of HER2 Expression and BindingCancer Discovery, 2026
2025
- Developing and benchmarking Sage 2.3.0 with the AshGC neural network charge model2025GitHub: https://github.com/openforcefield/ashgc-v1.0-fit
- Large-scale collaborative assessment of binding free energy calculations for drug discovery using OpenFE2025GitHub: https://github.com/OpenFreeEnergy/IndustryBenchmarks2024
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- The journey of data: Lessons learned in modeling kinase affinity, selectivity, and resistance [Article v1.0]Living Journal of Computational Molecular Science, 2025GitHub: https://github.com/openkinome/kinoml-techpaper-LiveCoMS
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- A structure-based computational pipeline for broad-spectrum antiviral discovery2025GitHub: https://github.com/choderalab/drugforge
- Open-science discovery of DNDI-6510, a compound that addresses genotoxic and metabolic liabilities of the COVID Moonshot SARS-CoV-2 Mpro lead inhibitor2025
- Prospective evaluation of structure-based simulations reveal their ability to predict the impact of kinase mutations on inhibitor bindingThe Journal of Physical Chemistry B, 2025GitHub: https://github.com/openkinome/study-abl-resistance
- The Need for Continuing Blinded Pose- and Activity Prediction BenchmarksThe Journal of Chemical Information and Modeling, 2025
- Fine-tuning molecular mechanics force fields to experimental free energy measurements2025GitHub: https://github.com/choderalab/timemachine_hydration_paper
2024
- Neural network potentials for enabling advanced samll-molecule drug discovery and generative designGEN Biotechnology, 2024
- EspalomaCharge: Machine learning-enabled ultrafast partial charge assignmentJournal of Chemical Physics, 2024GitHub: https://github.com/choderalab/espaloma_charge
- DrugGym: A testbed for the economics of autonomous drug discovery2024GitHub: https://github.com/choderalab/drug-gym/
- Enhancing protein–ligand binding affinity predictions using neural network potentialsJournal of Chemical Information and Modeling, 2024GitHub: https://github.com/compsciencelab/ATM_benchmark/tree/main/ATM_With_NNPs
- Benchmarking Cross-Docking Strategies in Kinase Drug DiscoveryJournal of Chemical Information and Modeling, 2024GitHub: https://github.com/openkinome/kinase-docking-benchmark
- Nutmeg and SPICE: Models and data for biomolecular machine learningJournal of Chemical Theory and Computation, 2024GitHub: https://github.com/openmm/spice-dataset
- Machine-learned molecular mechanics force fields from large-scale quantum chemical dataChemical Science, 2024GitHub: https://github.com/choderalab/espaloma-0.3.0-manuscript
2023
- OpenMM 8: molecular dynamics simulation with machine learning potentialsJournal of Physical Chemistry B, 2023GitHub: http://openmm.org
- SPICE, a dataset of drug-like molecules and peptides for training machine learning potentialsScientific Data, 2023GitHub: https://github.com/openmm/spice-dataset
2022
- MEN1 mutations mediate clinical resistance to Menin inhibitionNature, 2022GitHub: https://github.com/choderalab/men1
- Development and benchmarking of Open Force Field 2.0.0—the Sage small molecule force field2022GitHub: https://github.com/openforcefield/openff-sage
- Open Force Field BespokeFit: Automating bespoke torsion parametrization at scale2022GitHub: https://github.com/openforcefield/openff-bespokefit
- Improving force field accuracy by training against condensed phase mixture propertiesJournal of Chemical Theory and Computation, 2022GitHub: https://github.com/SimonBoothroyd/binary-mixture-publication
- The Open Force Field Evaluator: An automated, efficient, and scalable framework for the estimation of physical properties from molecular simulationJournal of Chemical Theory and Computation, 2022GitHub: https://github.com/openforcefield/openff-evaluator
- SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-predictionJournal of Computer Aided Molecular Design, 2022GitHub: https://github.com/samplchallenges/SAMPL7/tree/master/protein_ligand
- CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-findingNature Reviews Chemistry, 2022
- Bayesian inference-driven model parameterization and model selection for 2CLJQ fluid modelsJournal of Chemical Informatics and Modeling, 2022GitHub: https://github.com/SimonBoothroyd/bayesiantesting/tree/combined_run
- GCN2 kinase activation by ATP-competitive kinase inhibitorsNature Chemical Biology, 2022GitHub: https://github.com/cot2005/Tang_et_al_2021
- INK4 Tumor Suppressor Proteins Mediate Resistance to CDK4/6 Kinase InhibitorsCancer Discovery, 2022GitHub: https://github.com/choderalab/CDK_PROTAC
2021
- Teaching free energy calculations to learn from experimental data2021GitHub: https://github.com/choderalab/neutromeratio
- SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escapeNature, 2021GitHub: https://github.com/choderalab/rbd-ab-contact-analysis
- Discovery of SARS-CoV-2 main protease inhibitors using a synthesis-directed de novo design modelJournal of Computer-Aided Molecular Design, 2021
- Mutation in Abl kinase with altered drug binding kinetics indicates a novel mechanism of imatinib resistanceProceedings of the National Academy of Science, 2021GitHub: https://github.com/choderalab/Abl_kinase_N368S
- Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictionsJournal of Computer-Aided Molecular Design, 2021GitHub: https://github.com/samplchallenges/SAMPL6
- Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunityCell, 2021
- What Markov State Models can and cannot do: Correlation versus path-based observables in protein-folding modelsJournal of Chemical Theory and Computation, 2021GitHub: https://github.com/choderalab/msm-mfpt
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- SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteomeNature Chemistry, 2021
2020
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- Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P ChallengeJournal of Computer Aided Molecular Design, 2020GitHub: https://github.com/samplchallenges/SAMPL6
- Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric statesJournal of Computer-Aided Molecular Design, 2020GitHub: https://github.com/choderalab/titrato
- The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculationsJournal of Computer Aided Molecular Design, 2020GitHub: https://github.com/samplchallenges/SAMPL6/tree/master/host_guest/SAMPLing
2019
- Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challengeJournal of Computer Aided Molecular Design, 2019
- A small-molecule pan-Id antagonist inhibits pathologic ocular neovascularizationCell Reports, 2019
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- Ancestral reconstruction reveals mechanisms of ERK regulatory evolutioneLife, 2019GitHub: https://github.com/choderalab/ERK-ancestral-materials
- Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field InitiativeJournal of Chemical Theory and Computation, 2019GitHub: https://slochower.github.io/smirnoff-host-guest-manuscript/#code-and-data-availability
- Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemiaNature Communications, 2019GitHub: https://github.com/choderalab/musashi
- The dynamic conformational landscapes of the protein methyltransferase SETD8eLife, 2019GitHub: https://github.com/choderalab/SETD8-materials
- What makes a kinase promiscuous for inhibitors?Cell Chemical Biology, 2019GitHub: https://github.com/choderalab/DDR1_and_kinase_promiscuity_materials
2018
- OpenPathSampling: A Python framework for path sampling simulations. II. Building and customizing path ensembles and sample schemesJournal of Chemical Theory and Computation, 2018GitHub: https://github.com/openpathsampling/openpathsampling
- Toward learned chemical perception of force field typing rulesJournal of Chemical Theory and Computation, 2018GitHub: https://github.com/openforcefield/smarty
- Overview of the SAMPL6 host-guest binding affinity prediction challengeJournal of Computer-Aided Molecular Design special issue on SAMPL6, 2018
- An open library of human kinase domain constructs for automated bacterial expressionBiochemistry, 2018
- pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragmentsJournal of Computer-Aided Molecular Design special issue on SAMPL6, 2018
- Acquired resistance to IDH inhibition through trans or cis dimer-interface mutationsNature, 2018
- Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculationsCommunications Biology, 2018
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- Quantifying configuration-sampling error in Langevin simulations of complex molecular systemsentropy, 2018
- Escaping atom types in force fields using direct chemical perceptionJournal of Chemical Theory and Computation, 2018
- A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylationeLife, 2018
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- Biomolecular simulations under realistic macroscopic salt conditionsJournal of Physical Chemistry B, 2018
- Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte CarloJournal of Physical Chemistry B, 2018
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2017
- OpenMM 7: Rapid Development of High Performance Algorithms for Molecular DynamicsPLoS Computational Biology, 2017
- Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv databaseJournal of Chemical Engineering Data, 2017
- L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pHNature Chemical Biology, 2017
- A water-mediated allosteric network governs activation of Aurora kinase ANature Chemical Biology, 2017
- Results of the 2017 Roadmap survey of the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenge communityUC Irvine escholarship.org, 2017
2016
- Mechanistically distinct cancer-associated mTOR activation clusters predict sensitivity to rapamycinJournal of Clinical Investigation, 2016
- Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challengeJournal of Computer-Aided Molecular Design, 2016
- Ensembler: Enabling high-throughput molecular simulations at the superfamily scalePLoS Computational Biology, 2016
- A simple method for automated equilibration detection in molecular simulationsJournal of Chemical Theory and Computation, 2016
2015
- Modeling error in experimental assays using the bootstrap principle: Understanding discrepancies between assays using different dispensing technologiesJournal of Computer Aided Molecular Design, 2015
- Avoiding accuracy-limiting pitfalls in the study of protein-ligand interactions with isothermal titration calorimetryManuscript prior to submission, 2015
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- Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data ArchiveJournal of Physical Chemistry B, 2015
2014
- Markov state models of biomolecular conformational dynamicsCurrent Opinion in Structural Biology, 2014
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- Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systemsJournal of Physical Chemistry B, 2014
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2013
- Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamicsJournal of Computer-Aided Molecular Design, 2013
- Systematic improvement of a classical molecular model of waterJournal of Physical Chemistry B, 2013
- Entropy-enthalpy compensation: Role and ramifications for rational ligand designAnnual Review of Biophysics, 2013
- Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium discrete Langevin dynamics simulationsPhysical Review X, 2013
2012
- OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulationJournal of Chemical Theory and Computation, 2012
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- On the use of experimental observations to bias simulated ensemblesJournal of Chemical Theory and Computation, 2012
- The molten globule state is unusually deformable under mechanical forceProceedings of the National Academy of Sciences USA, 2012
2011
- Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixingJournal of Chemical Physics, 2011
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- Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulationProceedings of the National Academy of Sciences USA, 2011
- Splitting probabilities as a test of reaction coordinate choice in single-molecule experimentsPhysical Review Letters, 2011
- A robust approach to estimating rates from time-correlation functionsPreprint ahead of submission, 2011
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- Bayesian hidden Markov model analysis of single-molecule force spectroscopy: Characterizing kinetics under measurement uncertaintypreprint, 2011
- Systematic errors in isothermal titration calorimetry: Concentrations and baselinesAnalytical Biochemistry, 2011
- Dynamical reweighting: Improved estimates for dynamical properties from simulations at multiple temperaturesJournal of Chemical Physics, 2011
- Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamicsJournal of Chemical Physics, 2011
- Markov models of molecular kinetics: Generation and validationJournal of Chemical Physics, 2011
- Free energy methods in drug discovery and design: Progress and challengesCurrent Opinion in Structural Biology, 2011
- Dynamical fingerprints: A theoretical framework for understanding biomolecular processes by combination of simulation and kinetic experimentsProceedings of the National Academy of Sciences USA, 2011
- Estimating equilibrium ensemble averages using multiple time slices from driven nonequilibrium processesJournal of Chemical Physics, 2011
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- Alchemical free energy methods for drug discovery: progress and challengesCurrent Opinion in Structural Biology, 2011
2010
- Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolutionJournal of Chemical Physics, 2010
- The mechanical properties of PCNA: Implications for the loading and function of a DNA sliding clampBiophysical Journal, 2010
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2009
- Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averagesJournal of Chemical Physics, 2009
- Bayesian comparison of Markov models of molecular dynamics with detailed balance constraintJournal of Chemical Physics, 2009
2008
- Statistically optimal analysis of samples from multiple equilibrium statesJournal of Chemical Physics, 2008
- Technical Report: Self-consistent definition and computation of the electrostatic field for the Amber and related forcefields with particle-mesh EwaldTechnical Report, 2008
- Predicting small-molecule solvation free energies: A blind challenge test for computational chemistryJournal of Medicinal Chemistry, 2008
- Treating entropy and conformational changes in implicit solvent simulations of small moleculesJournal of Physical Chemistry B, 2008
2007
- Accurate and efficient corrections for missing dispersion interactions in molecular simulationsJournal of Physical Chemistry B, 2007
- Alchemical free energy calculations: Ready for prime time?Annual Reports in Computational Chemistry, 2007
- Predicting absolute ligand binding free energies to a simple model siteJournal of Molecular Biology, 2007
- The protein folding problem: When will it be solved?Current Opinion in Structural Biology, 2007
- Confine-and-release method: Obtaining correct binding free energies in the presence of protein conformational changeJournal of Chemical Theory and Computation, 2007
- Protein Folding by Zipping and AssemblyProceedings of the National Academy of Sciences USA, 2007
- Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamicsJouyrnal of Chemical Physics, 2007
- Comparison of charge models for fixed-charge force fields: Small-molecule hydration free energies in explicit solventJournal of Physical Chemistry B, 2007
- Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulationsJournal of Chemical Theory and Computation, 2007
2006
- Long-time protein folding dynamics from short-time molecular dynamics simulationsMultiscale Modeling & Simulation, 2006
- On the use of orientational restraints and symmetry corrections in alchemical free energy calculationsJournal of Chemical Physics, 2006
- Master equation models of macromolecular dynamics from atomistic simulationUCSF Dissertation, 2006
2004
- Technical report: An integrated system for executing and analyzing large-scale molecular dynamics simulationsUCSF, 2004
- Constructing master equation models of protein folding and dynamics from atomistic simulationProtein Science, 2004
2002
- MOPED: Method for optimizing physical energy parameters using decoysJournal of Computational Chemistry, 2002
2001
- An alternative explanation for the catalytic proficiency of orotidine 5’-phosphate decarboxylaseJournal of the American Chemical Society, 2001