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John D. Chodera, Ph.D.

1999-2006 Graduate Group in Biophysics University of California, San Francisco, San Francisco, CA 
 2007-2008 Chemistry Stanford University, Palo Alto, CA 
 2008-2012 QB3 University of California, Berkeley, Berkeley, CA, United States 
 2012- Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center, Rockville Centre, NY, United States 
drug discovery, computational biophysics, protein folding and stability
"John Chodera"
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William C. Swope research assistant 2005-2005 IBM Research - Almaden
 (IBM Research Predoctoral Fellowship)
Ken A. Dill grad student 2006 UCSF
 (Master equation models of macromolecular dynamics from atomistic simulation.)
Vijay S. Pande post-doc 2007-2008 Stanford
Phillip L. Geissler post-doc 2008-2012 UC Berkeley
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Zhang I, Rufa DA, Pulido I, et al. (2023) Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex. Journal of Chemical Theory and Computation
Boothroyd S, Behara PK, Madin OC, et al. (2023) Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. Journal of Chemical Theory and Computation
Zhang I, Rufa DA, Pulido I, et al. (2023) Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex. Biorxiv : the Preprint Server For Biology
Perner F, Stein EM, Wenge DV, et al. (2023) MEN1 mutations mediate clinical resistance to menin inhibition. Nature
Outhwaite IR, Singh S, Berger BT, et al. (2023) Death by a Thousand Cuts â€" Combining Kinase Inhibitors for Selective Target Inhibition and Rational Polypharmacology. Biorxiv : the Preprint Server For Biology
Hahn DF, Bayly CI, Macdonald HEB, et al. (2022) Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1]. Living Journal of Computational Molecular Science. 4
Horton JT, Boothroyd S, Wagner J, et al. (2022) Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale. Journal of Chemical Information and Modeling
Boothroyd S, Madin OC, Mobley DL, et al. (2022) Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties. Journal of Chemical Theory and Computation
Boothroyd S, Wang LP, Mobley DL, et al. (2022) Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation. Journal of Chemical Theory and Computation
Grosjean H, Işık M, Aimon A, et al. (2022) SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction. Journal of Computer-Aided Molecular Design
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