John D. Chodera

发表

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

Frank Noé, David W. H. Swenson, Jan-Hendrik Prinz, 2018 .

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

David L. Mobley, John D. Chodera, Mehtap Işık, 2019, Journal of Computer-Aided Molecular Design.

MOPED: Method for optimizing physical energy parameters using decoys

J. Ben Rosen, Chaok Seok, John D. Chodera, 2003, J. Comput. Chem..

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

Michail Papadourakis, Stefano Bosisio, David L. Mobley, 2020, Journal of Computer-Aided Molecular Design.

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

Sean Ekins, John D. Chodera, Sonya M. Hanson, 2015, bioRxiv.

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

Hannes H. Loeffler, David L. Mobley, John D. Chodera, 2017 .

OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics

Robert T. McGibbon, Vijay S. Pande, Matthew P. Harrigan, 2016 .

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

Christian Kramer, Terry R. Stouch, John D. Chodera, 2015, Journal of Computer-Aided Molecular Design.

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

Frank Noé, David W. H. Swenson, Jan-Hendrik Prinz, 2018, bioRxiv.

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

John D. Chodera, Kyle A. Beauchamp, Sonya M. Hanson, 2015, bioRxiv.

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

David L. Mobley, John D. Chodera, Mehtap Işık, 2020, Journal of Computer-Aided Molecular Design.

End-to-End Differentiable Molecular Mechanics Force Field Construction pdf

Yuanqing Wang, John D. Chodera, Josh Fass, 2020, ArXiv.

Overview of the SAMPL6 host–guest binding affinity prediction challenge

David L. Mobley, Michael Chiu, Michael K. Gilson, 2018, bioRxiv.

What Markov state models can and cannot do: Correlation versus path-based observables in protein folding models

Frank Noé, Daniel M. Zuckerman, John D. Chodera, 2020, bioRxiv.

Sharing Data from Molecular Simulations

Alexandre M. J. J. Bonvin, Helmut Grubmüller, Erik Lindahl, 2019, J. Chem. Inf. Model..

Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge

David L. Mobley, John D. Chodera, Daniel F. Ortwine, 2016, bioRxiv.

SARS-CoV-2 Simulations go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome

John D. Chodera, Vincent A. Voelz, Gregory R. Bowman, 2021, Biophysical Journal.

Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states

John D. Chodera, Mehtap Işık, Ariën S. Rustenburg, 2020, Journal of Computer-Aided Molecular Design.

SARS-CoV-2 Simulations Go Exascale to Capture Spike Opening and Reveal Cryptic Pockets Across the Proteome

John D. Chodera, Vincent A. Voelz, Gregory R. Bowman, 2020, bioRxiv.

Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0.1

David L. Mobley, Michael K. Gilson, Christopher I. Bayly, 2018, bioRxiv.

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

John D. Chodera, Ken A. Dill, Jed W. Pitera, 2006, Multiscale Model. Simul..

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

Xiao Wang, David L. Mobley, John D. Chodera, 2018, bioRxiv.

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

Benedict J. Leimkuhler, John D. Chodera, David A. Sivak, 2018, bioRxiv.

A simple method for automated equilibration detection in molecular simulations

John D. Chodera, 2015 .

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

David L. Mobley, Michael K. Gilson, Christopher I. Bayly, 2020 .

Systematic Improvement on the Classical Molecular Model of Water

Vijay S. Pande, John D. Chodera, Jay W. Ponder, 2014 .

Quantifying configuration-sampling error in Langevin simulations of complex molecular systems

Benedict Leimkuhler, John D. Chodera, David A. Sivak, 2018 .

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

Vijay S. Pande, Matthew P. Harrigan, Bernard R. Brooks, 2016, bioRxiv.

Is structure based drug design ready for selectivity optimization?

Robert Abel, Lingle Wang, John D. Chodera, 2020, bioRxiv.

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

Kai Wang, John D. Chodera, Michael R. Shirts, 2013, Journal of Computer-Aided Molecular Design.

Overview of the SAMPL6 host-guest binding affinity prediction challenge

Wei Yao, David L. Mobley, Michael K. Gilson, 2018, bioRxiv.

Ensembler: Enabling high-throughput molecular simulations at the superfamily scale

John D. Chodera, Kyle A. Beauchamp, Sonya M. Hanson, 2015 .

NNP/MM: Fast molecular dynamics simulations with machine learning potentials and molecular mechanics

Gianni De Fabritiis, Roberto Fino, John D. Chodera, 2022, ArXiv.

Bayesian-Inference-Driven Model Parametrization and Model Selection for 2CLJQ Fluid Models

United Kingdom, John D. Chodera, Boulder, 2021, J. Chem. Inf. Model..

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

David L. Mobley, John D. Chodera, Mehtap Işık, 2021, Journal of Computer-Aided Molecular Design.

Alchemical Free Energy Calculations : Ready for Prime Time ?

David L. Mobley, John D. Chodera, Michael R. Shirts, 2016 .

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

Bo Wang, John D. Chodera, Steven K. Albanese, 2018, Nature.

Avoiding accuracy-limiting pitfalls in the study of protein-ligand interactions with isothermal titration calorimetry

John D. Chodera, Joel Tellinghuisen, J. Chodera, 2015, bioRxiv.

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

Robert Abel, Lingle Wang, Kevin Hauser, 2017, Communications Biology.

Microsecond molecular dynamics simulation of kinase domain of the human tyrosine kinase ABL1

John D. Chodera, Sonya M. Hanson, 2016 .

A robust approach to estimating rates from time-correlation functions

Vijay S. Pande, John D. Chodera, William C. Swope, 2011, 1108.2304.

Bayesian hidden Markov model analysis of single-molecule force spectroscopy: Characterizing kinetics under measurement uncertainty

John D. Chodera, Bettina Keller, Nina Singhal Hinrichs, 2011, 1108.1430.

The Dynamic Conformational Landscapes of the Protein Methyltransferase SETD8

Cheng Luo, Jian Jin, Hualiang Jiang, 2018, bioRxiv.

Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems

John D. Chodera, David A. Sivak, Gavin E. Crooks, 2013, The journal of physical chemistry. B.

Biomolecular Simulations under Realistic Macroscopic Salt Conditions

Gregory A Ross, John D. Chodera, Patrick B. Grinaway, 2017 .

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

David L. Mobley, John D. Chodera, Mehtap Işık, 2019, bioRxiv.

Chapter 4 Alchemical Free Energy Calculations: Ready for Prime Time?

David L. Mobley, John D. Chodera, Michael R. Shirts, 2007 .

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)]

David D. L. Minh, John D. Chodera, 2012 .

Quantitative Self-Assembly Prediction Yields Targeted Nanomedicines

John D. Chodera, Mehtap Işık, Januka Budhathoki-Uprety, 2017, Nature Materials.

Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge

David L. Mobley, John D. Chodera, Daniel F. Ortwine, 2016 .

Using Nonequilibrium Fluctuation Theorems to Understand and Correct Errors in Equilibrium and Nonequ

John D. Chodera, David A. Sivak, Gavin E. Crooks, 2011, 1107.2967.