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John D. Chodera, Ph.D.

Affiliations:	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

Area:

drug discovery, computational biophysics, protein folding and stability

Website:

http://choderalab.org

Google:

Mean distance: 9.43

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Parents

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

Children

Hersh V Gupta	research assistant	2017-2020	Memorial Sloan Kettering Cancer Center
Kendall Lemons	grad student
Alexander Matthew Payne	grad student	2020-	Memorial Sloan Kettering Cancer Center (Microtree)
Sukrit Singh	post-doc		Memorial Sloan Kettering Cancer Center

Collaborators

BETA: Related publications

Publications

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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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