List of works - John D. Chodera

A Simple Method for Automated Equilibration Detection in Molecular Simulations.

scientific article

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

scientific article published on 21 February 2018

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

scientific article published on 6 February 2017

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

scientific article published on 26 July 2018

Ancestral reconstruction reveals mechanisms of ERK regulatory evolution

scientific article published on 13 August 2019

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

scientific article published on 24 April 2017

Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge

scientific article published on 27 February 2020

Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

scientific article published in PLoS ONE

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

scientific article published in July 2009

Best Practices for Alchemical Free Energy Calculations [Article v1.0]

scientific article published in 2020

Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0]

scientific article published in 2022

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

scientific article published on 12 March 2018

Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

scientific article published on 25 October 2019

Biomolecular Simulations Under Realistic Macroscopic Salt Conditions.

scientific article published on 13 April 2018

Comparison of Charge Models for Fixed-Charge Force Fields: Small Molecule Hydration Free Energies in Explicit Solvent

Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field

scientific article published on 22 September 2021

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

scientific article

Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design ⬇️

scientific article published on January 1, 2013

Escaping atom types in force fields using direct chemical perception

scientific article published on 30 October 2018

Estimation and validation of Markov models.

scientific article published on January 2014

Hypoxia Induces Production of L-2-Hydroxyglutarate.

scientific article published on 23 July 2015

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

scientific article

Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties

scientific article published on 09 May 2022

Introduction to the special issue: Data Part 2: Experimental Data

scientific article published in October 2015

Is Structure-Based Drug Design Ready for Selectivity Optimization?

scientific article published on 29 October 2020

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

scientific article published on 6 March 2017

Limitations of constant-force-feedback experiments

scientific article

Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations

article

MEN1 mutations mediate clinical resistance to menin inhibition

scientific article published on 15 March 2023

MOPED: method for optimizing physical energy parameters using decoys.

scientific article published in January 2003

Markov state models of biomolecular conformational dynamics

scientific article

Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge

scientific article published on 7 October 2016

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

scientific article published on 02 August 2016

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

scientific article

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

scientific article published on 24 October 2011

Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge

scientific article published on 19 December 2019

On the Use of Experimental Observations to Bias Simulated Ensembles

scientific article published on 27 August 2012

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

scientific article

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale

scientific article published in 2022

Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation

scientific article published on 04 May 2022

Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors

scientific article published on 10 November 2023

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

scientific article

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

scientific article

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

scientific article published on 31 December 2018

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

article

Overview of the SAMPL6 host-guest binding affinity prediction challenge

scientific article published on 01 October 2018

Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions

scientific article published on 04 January 2021

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

scientific article published on 13 June 2018

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

scientific article published on 26 April 2018

Quantitative self-assembly prediction yields targeted nanomedicines.

scientific article

Sharing Data from Molecular Simulations

scientific article published on 11 October 2019

Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia.

scientific article

Spectral Rate Theory for Two-State Kinetics

scientific article published on February 2014

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

scientific article

Statistically optimal analysis of samples from multiple equilibrium states

scientific article published in September 2008

Systematic errors in isothermal titration calorimetry: concentrations and baselines

scientific article published on 26 March 2011

Systematic improvement of a classical molecular model of water

scientific article published on 14 August 2013

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

scientific article published on 27 January 2020

The dynamic conformational landscape of the protein methyltransferase SETD8.

scientific article published on 13 May 2019

The molten globule state is unusually deformable under mechanical force.

scientific article published on 21 February 2012

The ribosome modulates nascent protein folding

scientific article

The social network (of protein conformations)

scientific article

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

scientific article

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

scientific article

Toward Learned Chemical Perception of Force Field Typing Rules

scientific article published on 24 December 2018

Treating entropy and conformational changes in implicit solvent simulations of small molecules

scientific article published on 3 January 2008

Uncertainty estimation

scientific article published in January 2014

What Makes a Kinase Promiscuous for Inhibitors?

scientific article published on 03 January 2019

What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models

scientific article published on 28 April 2021

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

scientific article published on 01 October 2018

List of works by John D. Chodera

A Simple Method for Automated Equilibration Detection in Molecular Simulations.

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

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

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

Ancestral reconstruction reveals mechanisms of ERK regulatory evolution

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

Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge

Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint

Best Practices for Alchemical Free Energy Calculations [Article v1.0]

Best Practices for Constructing, Preparing, and Evaluating Protein-Ligand Binding Affinity Benchmarks [Article v1.0]

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

Binding Thermodynamics of Host-Guest Systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative

Biomolecular Simulations Under Realistic Macroscopic Salt Conditions.

Comparison of Charge Models for Fixed-Charge Force Fields: Small Molecule Hydration Free Energies in Explicit Solvent

Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field

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

Entropy-Enthalpy Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design ⬇️

Escaping atom types in force fields using direct chemical perception

Estimation and validation of Markov models.

Hypoxia Induces Production of L-2-Hydroxyglutarate.

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

Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties

Introduction to the special issue: Data Part 2: Experimental Data

Is Structure-Based Drug Design Ready for Selectivity Optimization?

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

Limitations of constant-force-feedback experiments

Long‐Time Protein Folding Dynamics from Short‐Time Molecular Dynamics Simulations

MEN1 mutations mediate clinical resistance to menin inhibition

MOPED: method for optimizing physical energy parameters using decoys.

Markov state models of biomolecular conformational dynamics

Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge

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

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

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

Octanol-water partition coefficient measurements for the SAMPL6 blind prediction challenge

On the Use of Experimental Observations to Bias Simulated Ensembles

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale

Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation

Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors

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

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

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

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

Overview of the SAMPL6 host-guest binding affinity prediction challenge

Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions

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

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

Quantitative self-assembly prediction yields targeted nanomedicines.

Sharing Data from Molecular Simulations

Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia.

Spectral Rate Theory for Two-State Kinetics

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

Statistically optimal analysis of samples from multiple equilibrium states

Systematic errors in isothermal titration calorimetry: concentrations and baselines

Systematic improvement of a classical molecular model of water

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

The dynamic conformational landscape of the protein methyltransferase SETD8.

The molten globule state is unusually deformable under mechanical force.

The ribosome modulates nascent protein folding

The social network (of protein conformations)

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

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

Toward Learned Chemical Perception of Force Field Typing Rules

Toward Learned Chemical Perception of Force Field Typing Rules

Toward Learned Chemical Perception of Force Field Typing Rules

Toward Learned Chemical Perception of Force Field Typing Rules

Toward Learned Chemical Perception of Force Field Typing Rules

Treating entropy and conformational changes in implicit solvent simulations of small molecules

Uncertainty estimation

What Makes a Kinase Promiscuous for Inhibitors?

What Markov State Models Can and Cannot Do: Correlation versus Path-Based Observables in Protein-Folding Models

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