Specialties

Ronald M. Levy

Laura Carnell Professor
Theory/Computation

Office: SERC 718
Phone: 215-204-0607
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Biography

1976-1980

1976

1970

Selected Awards

Postdoctoral researcher, Harvard University

Ph.D. Harvard University

B.S. Reed College

Alfred P. Sloan Foundation Fellow. NIH Research Career Development Award. John Simon Guggenheim Foundation Fellowship. Japan Society for the Promotion of Science Fellowship. AAAS Fellow

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Interests

My research interests are focused on the development and application of computational methods for studying the structure, function, folding, and dynamics of proteins.  We work on problems involving the interplay between computational models in structural biology and experiments at different levels of resolution and different time scales from femtoseconds to seconds or longer.  Using computational statistical mechanics as a framework, we study solvation effects in chemistry and biophysics, and develop methods and effective potentials for simulating these systems.  Our recent work is focused on the development of novel free energy methods for modeling protein-ligand binding, allosteric conformational changes of proteins, and studying their energy and evolutionary landscapes.

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Select Publications

Simulating Replica Exchange: Markov State Models, Proposal Schemes and the Infinite Swapping Limit
Zhang, Bin W., Wei Dai, Emilio Gallicchio, Peng He, Junchao Xia, Zhiqiang Tan, and Ronald M. Levy
The Journal of Physical Chemistry B, 120, 8289 (2016)

Allosteric HIV-1 integrase inhibitors promote aberrant protein multimerization by directly mediating inter-subunit interactions: Structural and thermodynamic modeling studies
Deng, Nanjie, Ashley Hoyte, Yara E. Mansour, Mosaad S. Mohamed, James R. Fuchs, Allan N. Engelman, Mamuka Kvaratskhelia, and Ronald M. Levy
Protein Science, 25, 1911 (2016)

Structural propensities of kinase family proteins from a Potts model of residue co-variation
Haldane, Allan, William F. William, Peng He, R. S. K. Vijayan, and Ronald M. Levy
Protein Science, 25, 1378-1384 (2016)
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Conformational Analysis of the DFG-Out Kinase Motif and Biochemical Profiling of Structurally Validated Type II Inhibitors
Vijayan, R. S. K., Peng He, Vivek Modi, Krisna C. Duong-Ly, Haiching Ma, Jeffrey R. Peterson, Roland L. Dunbrack, and Ronald M. Levy
Journal of Medicinal Chemistry, 58, 466-479 (2015)

Molecular Dynamics of the Proline Switch and Its Role in Crk Signaling
Xia, Junchao and Ronald M. Levy
J. Phys. Chem. B, 118, 4535-4545 (2014)