John D. Chodera
#165,612
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Computational biologist
John D. Chodera's AcademicInfluence.com Rankings
John D. Choderachemistry Degrees
Chemistry
#4920
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#6014
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Organic Chemistry
#819
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#919
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John D. Choderabiology Degrees
Biology
#13405
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#16950
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Computational Biology
#309
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#310
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Biochemistry
#2345
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#2494
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Chemistry Biology
John D. Chodera's Degrees
- PhD Chemistry University of California, Berkeley
- Bachelors Chemistry University of California, Berkeley
Why Is John D. Chodera Influential?
(Suggest an Edit or Addition)John D. Chodera's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Statistically optimal analysis of samples from multiple equilibrium states. (2008) (1258)
- OpenMM 7: Rapid development of high performance algorithms for molecular dynamics (2016) (1117)
- Current status of the AMOEBA polarizable force field. (2010) (1023)
- Markov models of molecular kinetics: generation and validation. (2011) (924)
- Markov state models of biomolecular conformational dynamics. (2014) (560)
- Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. (2007) (559)
- OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation. (2013) (530)
- Alchemical free energy methods for drug discovery: progress and challenges. (2011) (444)
- Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity (2021) (443)
- Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations. (2007) (414)
- Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design. (2013) (387)
- Hypoxia Induces Production of L-2-Hydroxyglutarate. (2015) (354)
- Ensemble Docking in Drug Discovery. (2018) (273)
- Predicting absolute ligand binding free energies to a simple model site. (2007) (265)
- Systematic improvement of a classical molecular model of water. (2013) (265)
- Predicting small-molecule solvation free energies: an informal blind test for computational chemistry. (2008) (256)
- SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape (2021) (251)
- The protein folding problem: when will it be solved? (2007) (248)
- On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. (2006) (246)
- The Ribosome Modulates Nascent Protein Folding (2011) (237)
- Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent. (2007) (236)
- Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations (2006) (206)
- On the Use of Experimental Observations to Bias Simulated Ensembles. (2012) (198)
- Accurate and efficient corrections for missing dispersion interactions in molecular simulations. (2007) (184)
- Acquired resistance to IDH inhibition through trans or cis dimer-interface mutations (2018) (183)
- L-2-hydroxyglutarate production arises from non-canonical enzyme function at acidic pH (2017) (173)
- The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. (2007) (156)
- Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database (2017) (151)
- Chapter 4 Alchemical Free Energy Calculations: Ready for Prime Time? (2007) (149)
- Protein folding by zipping and assembly (2007) (143)
- Replica exchange and expanded ensemble simulations as Gibbs sampling: simple improvements for enhanced mixing. (2011) (138)
- A Simple Method for Automated Equilibration Detection in Molecular Simulations. (2016) (112)
- Quantitative Self-Assembly Prediction Yields Targeted Nanomedicines (2017) (110)
- Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments (2011) (105)
- Treating entropy and conformational changes in implicit solvent simulations of small molecules. (2008) (101)
- Escaping Atom Types in Force Fields Using Direct Chemical Perception. (2018) (98)
- Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics (2013) (97)
- Best Practices for Alchemical Free Energy Calculations [Article v1.0]. (2020) (95)
- Overview of the SAMPL6 host–guest binding affinity prediction challenge (2018) (95)
- The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations (2019) (75)
- The molten globule state is unusually deformable under mechanical force (2012) (75)
- Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia (2018) (74)
- SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome (2021) (74)
- Mechanistically distinct cancer-associated mTOR activation clusters predict sensitivity to rapamycin. (2016) (74)
- Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems. (2020) (73)
- Crowdsourcing drug discovery for pandemics (2020) (73)
- Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation (2011) (68)
- Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations (2017) (62)
- Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint. (2009) (58)
- Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field. (2020) (58)
- Dynamical reweighting: improved estimates of dynamical properties from simulations at multiple temperatures. (2011) (57)
- Systematic errors in isothermal titration calorimetry: concentrations and baselines. (2011) (56)
- Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems (2013) (56)
- Using Nonequilibrium Fluctuation Theorems to Understand and Correct Errors in Equilibrium and Nonequ (2011) (54)
- Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages. (2009) (52)
- Alchemical Free Energy Calculations : Ready for Prime Time ? (2016) (51)
- A water-mediated allosteric network governs activation of Aurora kinase A. (2017) (50)
- A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation (2017) (50)
- Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics. (2011) (48)
- Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo. (2018) (46)
- Limitations of constant-force-feedback experiments. (2012) (44)
- What Makes a Kinase Promiscuous for Inhibitors? (2019) (42)
- Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments. (2011) (42)
- Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge (2016) (42)
- Assessing the accuracy of octanol–water partition coefficient predictions in the SAMPL6 Part II log P Challenge (2020) (40)
- COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning (2020) (38)
- Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolution. (2010) (38)
- OpenPathSampling: A Python Framework for Path Sampling Simulations. 1. Basics (2018) (37)
- Towards chemical accuracy for alchemical free energy calculations with hybrid physics-based machine learning / molecular mechanics potentials (2020) (37)
- Citizen Scientists Create an Exascale Computer to Combat COVID-19 (2020) (36)
- Biomolecular Simulations under Realistic Macroscopic Salt Conditions (2017) (36)
- pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments (2018) (35)
- Toward Learned Chemical Perception of Force Field Typing Rules. (2018) (34)
- An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase. (2001) (33)
- SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome (2020) (31)
- OpenPathSampling: A Python Framework for Path Sampling Simulations. 2. Building and Customizing Path Ensembles and Sample Schemes (2018) (31)
- FOOTPRINT PATTERNS DURING WALKING (1973) (30)
- Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems (2018) (30)
- Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape (2021) (30)
- Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive. (2015) (29)
- A Small-Molecule Pan-Id Antagonist Inhibits Pathologic Ocular Neovascularization (2019) (27)
- The dynamic conformational landscape of the protein methyltransferase SETD8 (2019) (27)
- An Open Library of Human Kinase Domain Constructs for Automated Bacterial Expression. (2018) (26)
- Bayesian hidden Markov model analysis of single-molecule force spectroscopy: Characterizing kinetics under measurement uncertainty (2011) (26)
- Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0.1 (2018) (24)
- INK4 Tumor Suppressor Proteins Mediate Resistance to CDK4/6 Kinase Inhibitors (2021) (24)
- Octanol–water partition coefficient measurements for the SAMPL6 blind prediction challenge (2019) (24)
- The mechanical properties of PCNA: implications for the loading and function of a DNA sliding clamp. (2010) (22)
- Spectral Rate Theory for Two-State Kinetics. (2012) (21)
- Octanol-water partition coefficient measurements for the SAMPL6 Blind Prediction Challenge (2019) (20)
- Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative. (2019) (20)
- MOPED: Method for optimizing physical energy parameters using decoys (2003) (20)
- Sharing Data from Molecular Simulations (2019) (18)
- Avoiding accuracy-limiting pitfalls in the study of protein-ligand interactions with isothermal titration calorimetry (2015) (18)
- Ancestral reconstruction reveals mechanisms of ERK regulatory evolution (2019) (18)
- A white-knuckle ride of open COVID drug discovery (2021) (18)
- Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale (2015) (18)
- Uncertainty estimation. (2014) (18)
- Discovery of SARS-CoV-2 main protease inhibitors using a synthesis-directed de novo design model† (2021) (16)
- Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs (2021) (15)
- Overview of the SAMPL6 pKa Challenge: Evaluating small molecule microscopic and macroscopic pKa predictions (2020) (15)
- Bayesian analysis of isothermal titration calorimetry for binding thermodynamics (2018) (15)
- Open Science Discovery of Potent Non-Covalent SARS-CoV-2 Main Protease Inhibitors (2023) (15)
- 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. (2010) (15)
- What Markov state models can and cannot do: Correlation versus path-based observables in protein folding models (2020) (14)
- Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1]. (2021) (14)
- Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states (2020) (14)
- Pedobarographic Foot — Pressure Measurements and Their Applications (1979) (13)
- Analysis of gait from footprints. (1974) (13)
- The social network (of protein conformations) (2011) (12)
- Is structure based drug design ready for selectivity optimization? (2020) (12)
- Modeling error in experimental assays using the bootstrap principle: understanding discrepancies between assays using different dispensing technologies (2015) (11)
- Graph Nets for Partial Charge Prediction (2019) (10)
- GCN2 kinase activation by ATP-competitive kinase inhibitors (2021) (10)
- A robust approach to estimating rates from time-correlation functions (2011) (9)
- End-to-End Differentiable Molecular Mechanics Force Field Construction (2020) (9)
- Fitting quantum machine learning potentials to experimental free energy data: predicting tautomer ratios in solution (2020) (9)
- CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding (2021) (9)
- Open Science Discovery of Oral Non-Covalent SARS-CoV-2 Main Protease Inhibitors (2021) (9)
- Mutation in Abl kinase with altered drug-binding kinetics indicates a novel mechanism of imatinib resistance (2021) (8)
- openforcefield/openforcefields: Version 1.2.0 "Parsley" Update (2020) (8)
- Advancing predictive modeling through focused development of model systems to drive new modeling innovations (2016) (8)
- OpenPathSampling: A Python framework for path sampling simulations. I. Basics (2018) (8)
- SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials (2022) (8)
- Mutation in Abl kinase with altered drug binding kinetics indicates a novel mechanism of imatinib resistance (2021) (7)
- Capturing non-local through-bond effects when fragmenting molecules for quantum chemical torsion scans (2020) (7)
- Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation. (2021) (6)
- Overview of the SAMPL6 host-guest binding affinity prediction challenge (2018) (6)
- What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models. (2021) (6)
- Pedobarographic study of gait. (1980) (6)
- Estimation and validation of Markov models. (2014) (6)
- Erratum: Splitting Probabilities as a Test of Reaction Coordinate Choice in Single-Molecule Experiments [Phys. Rev. Lett. 107, 098102 (2011)] (2012) (5)
- MEN1 mutations mediate clinical resistance to menin inhibition (2023) (5)
- The Dynamic Conformational Landscapes of the Protein Methyltransferase SETD8 (2018) (4)
- Teaching free energy calculations to learn from experimental data (2021) (4)
- Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties. (2021) (3)
- Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models (2021) (3)
- openforcefield/openforcefields: Version 1.1.0 "Parsley" Update (2020) (3)
- Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge (2020) (3)
- SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction (2022) (3)
- End-to-end differentiable construction of molecular mechanics force fields (2022) (3)
- Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale (2022) (3)
- Driven Langevin dynamics: heat, work and pseudo-work (2011) (3)
- choderalab/openmmtools: 0.19.0 - Multiple alchemical regions (2019) (2)
- pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments (2018) (2)
- A simple method for automated equilibration detection in molecular simulations (2015) (2)
- Correction for Nilmeier et al., Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation (2012) (2)
- Why we are developing a patent-free Covid antiviral therapy (2021) (2)
- Capturing non-local through-bond effects in molecular mechanics force fields: II. Using fractional bond orders to fit torsion parameters (2022) (2)
- Numerical Langevin Simulations: Equilibrium Dynamics and Nonequilibrium Thermodynamics (2014) (2)
- OpenPathSampling: A Python framework for path sampling simulations. II. Building and customizing path ensembles and sample schemes (2018) (2)
- 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)] (2012) (2)
- Nonequilibrium candidate Monte Carlo: A new tool for equilibrium simulation (2011) (1)
- Nonequilibrium candidate Monte Carlo: A new tool for efficient equilibrium simulation (2011) (1)
- Results of the 2017 Roadmap survey of the Statistical Assessment of Modeling of Proteins and Ligands (SAMPL) challenge community (2017) (1)
- NNP/MM: Fast molecular dynamics simulations with machine learning potentials and molecular mechanics (2022) (1)
- Microsecond molecular dynamics simulation of kinase domain of the human tyrosine kinase ABL1 (2016) (1)
- openforcefield/openforcefield: 0.8.0 Virtual Sites and Bond Interpolation (2020) (1)
- Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex (2023) (1)
- Spatial Attention Kinetic Networks with E(n)-Equivariance (2023) (1)
- Best Practices for Alchemical Free Energy Calculations [Article v1.0] (2019) (1)
- Conformational Dynamics of Histone Methyltransferase SET8 Probed by Millisecond-Timescale Molecular Dynamics, Markov State Modeling and Biochemical Experiments (2018) (1)
- Capturing non-local through-bond effects in molecular mechanics force fields I: Fragmenting molecules for quantum chemical torsion scans [Article v1.1] (2022) (1)
- Automated high throughput pKa and distribution coefficient measurements of pharmaceutical compounds for the SAMPL8 blind prediction challenge (2021) (1)
- Mobleylab/Freesolv: Version 0.5 (2017) (1)
- Protein design using expanded ensembles (2016) (0)
- Spectral rate theory for projected two-state kinetics (2013) (0)
- Development and benchmarking of an open, self-consistent force field for proteins and small molecules from the open force field initiative. (2023) (0)
- Benchmarking and Optimizing Atomistic Forcefields with Density Measurements (2015) (0)
- ERK ancestral reconstruction (2019) (0)
- An open library of human kinase domain constructs for automated bacterial expression (2016) (0)
- Building an open, self-consistent force field for biopolymers and small molecules with the open force field initiative infrastructure (2022) (0)
- Bridging the Gap between Computation and Experiments in GPCRs (2016) (0)
- Choderalab/Pymbar: Fix Pypi Release (2017) (0)
- Can we Automatically Detect Biologically Relevant Order Parameters in Molecular Simulation? Comparing Long Timescale Simulations of Multiple Kinases (2017) (0)
- G Protein Signaling in Plants: Characterization of Alpha and Gamma Subunits (2017) (0)
- No Job Name (0)
- Driven Langevin systems: fluctuation theorems and faithful dynamics (2014) (0)
- Simulating mTOR Hyperactivating Mutations to Understand Functionally Significant Structural Rearrangements (2016) (0)
- Fast, conformation-independent charges with graph convolutional networks. (2023) (0)
- Spectral rate theory (2012) (0)
- Spectral rate theory-Supplementary Information (2012) (0)
- Abstract 4975: A small molecule pan Id protein antagonist shows strong antitumor activity (2017) (0)
- openmmtools: Release 0.8.1 - bugfix release (2016) (0)
- Introduction to the special issue: Data Part 2: Experimental Data (2015) (0)
- Open-Forcefield-Group/Openforcefield: 0.0.1 (2017) (0)
- Acquired resistance to IDH inhibition through trans or cis dimer-interface mutations (2018) (0)
- Conformational Dynamics of Histone Lysine Methyltransferases by Millisecond-Timescale Molecular Dynamics on Folding@home (2017) (0)
- Death by a Thousand Cuts – Combining Kinase Inhibitors for Selective Target Inhibition and Rational Polypharmacology (2023) (0)
- Histone Lysine Methyltransferases – conformational dynamics and selective inhibitor design (2016) (0)
- The rapidly expanding body of available genomic and protein structural data provides a rich resource for understanding protein dynamics with biomolecular simulation. While computational infrastructure has grown rapidly, simulations on anomicsscale are not yet widespread, primarily because soware (2015) (0)
- Abstract SY43-01: Stereochemistry matters: L-2HG as a tumor response to hypoxia (2015) (0)
- choderalab/openmm-forcefields: Updated AMBER force fields (AmberTools 19.9) and small molecule support via GAFF (2020) (0)
- Markov Models of Functional Dynamics of Histone Lysine Methyltransferases by Millisecond-Timescale Molecular Simulation and Chemical Probing (2019) (0)
- Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations (2018) (0)
- Choderalab/Yank: 0.19.4 - Schema And Parallel Setup Fixes (2017) (0)
- Technical Self-consistent definition and computation of the electrostatic field for the Amber and related forcefields with particle-mesh Ewald (2008) (0)
- 1 A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop 1 phosphorylation 2 3 (2017) (0)
- Hypoxia Induces Productio n of L-2-Hydroxyglutarate Graphical Abstract Highlights (0)
- What Makes a Kinase Promiscuous for Inhibitors ? Graphical Abstract Highlights (2019) (0)
- Dissecting the Contribution of Kinase Conformational Reorganization Energies to Inhibitor Selectivity (2016) (0)
- Choderalab/Aura-Materials: Elife Phosphorylation Paper (2018) (0)
- Choderalab/Openmoltools: Service Release (2016) (0)
- Author response: The dynamic conformational landscape of the protein methyltransferase SETD8 (2019) (0)
- Bayesian Active Drug Discovery (2020) (0)
- Automated High Throughput pKa and Distribution Coefficient Measurements of Pharmaceutical Compounds for the SAMPL8 Blind Prediction Challenge AUTHOR NAMES (2021) (0)
- Turning high-throughput structural biology into predictive inhibitor design (2021) (0)
- Abstract PO029: Targeting non-canonical Hippo pathway in NRF2-mutant liver cancer (2022) (0)
- Development and Benchmarking of 1 Open Force Field v1.0.0, the Parsley 2 small molecule force field 3 (2020) (0)
- EspalomaCharge: Machine learning-enabled ultra-fast partial charge assignment (2023) (0)
- Toward a Global View of the Conformational Landscape of the Human Kinome (2014) (0)
- Author response: Ancestral reconstruction reveals mechanisms of ERK regulatory evolution (2019) (0)
- Nonequilibrium candidate Monte Carlo: A new tool for e(cid:14)cient equilibrium simulation (2011) (0)
- openmmtools: Release 0.8.2 - bugfix release (2016) (0)
- Developing High-Throughput Fluorescence-Based Assays for Measuring Kinase Inhibitor Free Energies of Binding (2015) (0)
- Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia (2019) (0)
- Explorer The SAMPL 6 SAMPLing challenge (2020) (0)
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What Schools Are Affiliated With John D. Chodera?
John D. Chodera is affiliated with the following schools:
