John D. Chodera

Research interests

Publications

• MEN1 mutations mediate clinical resistance to menin inhibition

  Nature · 2023 · https://doi.org/10.1038/s41586-023-05755-9

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

  Science · 2023 · https://doi.org/10.1126/science.abo7201

• OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

  The Journal of Physical Chemistry B · 2023 · https://doi.org/10.1021/acs.jpcb.3c06662

• Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

  Cell · 2021 · https://doi.org/10.1016/j.cell.2021.01.037

• SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome

  Nature Chemistry · 2021 · https://doi.org/10.1038/s41557-021-00707-0

• SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape

  Nature · 2021 · https://doi.org/10.1038/s41586-021-03807-6

• Machine learning force fields and coarse-grained variables in molecular\n dynamics: application to materials and biological systems

  arXiv (Cornell University) · 2020 · https://doi.org/10.48550/arxiv.2004.06950

• Ensemble Docking in Drug Discovery

  Biophysical Journal · 2018 · https://doi.org/10.1016/j.bpj.2018.02.038

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

  PLoS Computational Biology · 2017 · https://doi.org/10.1371/journal.pcbi.1005659

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2016 · https://doi.org/10.1101/091801

• Hypoxia Induces Production of L-2-Hydroxyglutarate

  Cell Metabolism · 2015 · https://doi.org/10.1016/j.cmet.2015.06.023

• Markov state models of biomolecular conformational dynamics

  Current Opinion in Structural Biology · 2014 · https://doi.org/10.1016/j.sbi.2014.04.002

• Systematic Improvement of a Classical Molecular Model of Water

  The Journal of Physical Chemistry B · 2013 · https://doi.org/10.1021/jp403802c

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

  Annual Review of Biophysics · 2013 · https://doi.org/10.1146/annurev-biophys-083012-130318

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

  Journal of Chemical Theory and Computation · 2012 · https://doi.org/10.1021/ct300857j

• Alchemical free energy methods for drug discovery: progress and challenges

  Current Opinion in Structural Biology · 2011 · https://doi.org/10.1016/j.sbi.2011.01.011

• Markov models of molecular kinetics: Generation and validation

  The Journal of Chemical Physics · 2011 · https://doi.org/10.1063/1.3565032

• The Ribosome Modulates Nascent Protein Folding

  Science · 2011 · https://doi.org/10.1126/science.1209740

• Current Status of the AMOEBA Polarizable Force Field

  The Journal of Physical Chemistry B · 2010 · https://doi.org/10.1021/jp910674d

• Predicting Small-Molecule Solvation Free Energies: An Informal Blind Test for Computational Chemistry

  Journal of Medicinal Chemistry · 2008 · https://doi.org/10.1021/jm070549+

• Statistically optimal analysis of samples from multiple equilibrium states

  The Journal of Chemical Physics · 2008 · https://doi.org/10.1063/1.2978177

• Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

  The Journal of Chemical Physics · 2007 · https://doi.org/10.1063/1.2714538

• Predicting Absolute Ligand Binding Free Energies to a Simple Model Site

  Journal of Molecular Biology · 2007 · https://doi.org/10.1016/j.jmb.2007.06.002

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

  The Journal of Chemical Physics · 2006 · https://doi.org/10.1063/1.2221683

• Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations

  Journal of Chemical Theory and Computation · 2006 · https://doi.org/10.1021/ct0502864

Current projects

No projects listed.