Lista de obras - John D Chodera - Dominio Público Uruguay

A Simple Method for Automated Equilibration Detection in Molecular Simulations.

artículo científico publicado en 2016

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

artículo científico publicado en 2018

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

artículo científico publicado en 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

artículo científico publicado en 2019

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

artículo científico publicado en 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

artículo científico publicado en 2018

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

artículo científico publicado en 2009

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

artículo científico publicado en 2020

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

artículo científico publicado en 2022

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

artículo científico publicado en 2018

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

artículo científico publicado en 2019

Biomolecular Simulations Under Realistic Macroscopic Salt Conditions.

artículo científico publicado en 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

artículo científico publicado en 2021

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

artículo científico publicado en 2016

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

artículo científico publicado el 1 de enero de 2013

Escaping atom types in force fields using direct chemical perception

artículo científico publicado en 2018

Estimation and validation of Markov models.

artículo científico publicado en 2014

Hypoxia Induces Production of L-2-Hydroxyglutarate.

artículo científico publicado en 2015

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

artículo científico publicado en 2013

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

artículo científico publicado en 2022

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

artículo científico publicado en 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

artículo científico publicado en 2017

Limitations of constant-force-feedback experiments

artículo científico publicado en 2012

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.

artículo científico publicado en 2003

Markov state models of biomolecular conformational dynamics

artículo científico publicado en 2014

Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge

artículo científico publicado en 2016

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

artículo científico publicado en 2016

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

artículo científico publicado en 2015

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

artículo científico publicado en 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

artículo científico publicado en 2012

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

artículo científico publicado en 2006

Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale

artículo científico publicado en 2022

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

artículo científico publicado en 2022

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

artículo científico publicado en 2023

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

artículo científico publicado en 2012

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

artículo científico publicado en 2017

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

artículo científico publicado en 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

artículo científico

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

artículo científico publicado en 2018

Quantitative self-assembly prediction yields targeted nanomedicines.

artículo científico publicado en 2018

Sharing Data from Molecular Simulations

scientific article published on 11 October 2019

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

artículo científico publicado en 2019

Spectral Rate Theory for Two-State Kinetics

artículo científico publicado en 2014

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

artículo científico publicado en 2011

Statistically optimal analysis of samples from multiple equilibrium states

artículo científico publicado en 2008

Systematic errors in isothermal titration calorimetry: concentrations and baselines

artículo científico publicado en 2011

Systematic improvement of a classical molecular model of water

artículo científico publicado en 2013

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

artículo científico publicado en 2020

The dynamic conformational landscape of the protein methyltransferase SETD8.

artículo científico publicado en 2019

The molten globule state is unusually deformable under mechanical force.

artículo científico publicado en 2012

The ribosome modulates nascent protein folding

artículo científico publicado en 2011

The social network (of protein conformations)

artículo científico publicado en 2011

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

artículo científico publicado en 2014

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

artículo científico publicado en 2015

Toward Learned Chemical Perception of Force Field Typing Rules

artículo científico publicado en 2018

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

artículo científico publicado en 2008

Uncertainty estimation

artículo científico publicado en 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

artículo científico publicado en 2021

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

scientific article published on 01 October 2018

Lista de obras de 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