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The Chodera lab uses computation and experiments to develop quantitative, multiscale models of the effects of small molecules on biomolecular macromolecules and cellular pathways. To do this, the group utilizes physical models and rigorous statistical mechanics, with the overall goals of engineering novel therapeutics and tools for chemical biology, as well as understanding the physical driving forces behind ligand recognition the evolution of resistance mutations.

Publications

Entropy-enthalpy compensation: Role and ramifications for rational ligand design
John D. Chodera and David L. Mobley.
Annu. Rev. Biophys.42:121-142 (2013).
[ePrint] [DOI]

The ribosome modulates nascent protein folding
Christian Kaiser, Daniel H. Goldman,John D. Chodera, Ignacio Tinoco, Jr., and Carlos Bustamante.
Science 334:1723 (2011)
[DOI]

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation
Jerome P. Nilmeier, Gavin E. Crooks, David D. L. Minh, and John D. Chodera
Proc. Natl. Acad. Sci. USA, 108:E1009 (2011)
[DOI

Free energy methods in drug discovery and design: Progress and challenges
John D. Chodera, David L. Mobley, Michael R. Shirts, Richard W. Dixon Kim M. Branson, and Vijay S. Pande. 
Curr. Opin. Struct. Biol.21:150 (2011)
[DOI

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
John D. Chodera*, Nina Singhal*, William C. Swope, Vijay S. Pande, and Ken A. Dill. 
* These authors contributed equally to the work. 
J. Chem. Phys. 126(15):155101 (2007)
[DOI

Selected Achievements

Louis V. Gerstner Young Investigator Award (2013)

QB3-Berkeley Distinguished Postdoctoral Fellowship, University of California, Berkeley (2008)

IBM Predoctoral Fellowship (2005)

Howard Hughes Medical Institute Predoctoral Fellowship (2000)