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Chemistry

D-Index
69
Citations
26429
World Ranking
6074
National Ranking
1849

Overview

John D. Chodera is associated with Memorial Sloan Kettering Cancer Center in the United States. Their research primarily focuses on Biochemistry, Genetics, and Molecular Biology, with extensive work in Molecular Biology and Computational Theory and Mathematics. They also contribute to Materials Chemistry, Infectious Diseases, and Organic Chemistry.

The scientist's research covers key topics including:

  • Protein Structure and Dynamics
  • Computational Drug Discovery Methods
  • Machine Learning in Materials Science
  • SARS-CoV-2 and COVID-19 Research
  • Vaccines and Immunoinformatics Approaches
  • Enzyme Structure and Function
  • Mass Spectrometry Techniques and Applications

John D. Chodera has authored papers such as:

  • Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity, 2021, Cell
  • SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape, 2021, Nature
  • SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome, 2021, Nature Chemistry
  • OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials, 2023, The Journal of Physical Chemistry B
  • Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems, 2020, arXiv (Cornell University)

Their frequent co-authors include:

  • David L. Mobley
  • Pavan Kumar Behara
  • Michael R. Shirts
  • David Dotson
  • Sukrit Singh

Key venues for their publications are:

  • bioRxiv (Cold Spring Harbor Laboratory)
  • Zenodo (CERN European Organization for Nuclear Research)
  • arXiv (Cornell University)
  • Journal of Chemical Theory and Computation
  • Biophysical Journal

Best Publications

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

    Peter Eastman;Jason Swails;John D. Chodera;Robert T. McGibbon

  • Statistically optimal analysis of samples from multiple equilibrium states

    Michael R. Shirts;John D. Chodera

  • Current Status of the AMOEBA Polarizable Force Field

    Jay W. Ponder;Chuanjie Wu;Pengyu Ren;Vijay S. Pande

  • Markov models of molecular kinetics: Generation and validation

    Jan-Hendrik Prinz;Hao Wu;Marco Sarich;Bettina Keller

  • Markov state models of biomolecular conformational dynamics

    John D Chodera;Frank Noé

  • OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation

    Peter Eastman;Mark S. Friedrichs;John D. Chodera;Randall J. Radmer

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

    John D. Chodera;Nina Singhal;Vijay S. Pande;Ken A. Dill

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

    John D Chodera;David L Mobley;Michael R Shirts;Richard W Dixon

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

    John D. Chodera;David L. Mobley

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

    Emma C. Thomson;Emma C. Thomson;Laura E. Rosen;James G. Shepherd;Roberto Spreafico

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

    John D. Chodera;William C. Swope;Jed W. Pitera;Chaok Seok

  • Hypoxia Induces Production of L-2-Hydroxyglutarate

    Andrew M. Intlekofer;Raymond G. Dematteo;Sriram Venneti;Lydia W.S. Finley

  • Ensemble Docking in Drug Discovery.

    Rommie E. Amaro;Jerome Baudry;John Chodera;Özlem Demir

  • Systematic improvement of a classical molecular model of water.

    Lee Ping Wang;Teresa Head-Gordon;Jay W. Ponder;Pengyu Ren

  • Predicting absolute ligand binding free energies to a simple model site

    David L. Mobley;Alan P. Graves;John D. Chodera;Andrea C. McReynolds

  • OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

    Unknown

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

    David L. Mobley;John D. Chodera;Ken A. Dill

  • The protein folding problem: when will it be solved?

    Ken A Dill;S Banu Ozkan;Thomas R Weikl;John D Chodera

  • The Ribosome Modulates Nascent Protein Folding

    Christian M. Kaiser;Daniel H. Goldman;John D. Chodera;Ignacio Tinoco

  • Predicting small-molecule solvation free energies: an informal blind test for computational chemistry.

    Anthony Nicholls;David L. Mobley;J. Peter Guthrie;John D. Chodera

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

    David L Mobley;Elise Dumont;John D Chodera;Ken A Dill

  • Compensation: Role and Ramifications in Biomolecular Ligand Recognition and Design

    John D. Chodera;David L. Mobley

Frequent Co-Authors

Vijay S. Pande
Vijay S. Pande Stanford University
Ken A. Dill
Ken A. Dill Stony Brook University
Michael K. Gilson
Michael K. Gilson University of California, San Diego
Jesse D. Bloom
Jesse D. Bloom Fred Hutchinson Cancer Research Center
Erik Lindahl
Erik Lindahl Stockholm University
Marilyn R. Gunner
Marilyn R. Gunner City College of New York
Justin R. Cross
Justin R. Cross Memorial Sloan Kettering Cancer Center
Craig B. Thompson
Craig B. Thompson Memorial Sloan Kettering Cancer Center
Carlos Bustamante
Carlos Bustamante Stanford University

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