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.
The Relationship Between Solvation Thermodynamics from IST and DFT Perspectives.
Levy, Ronald M., Di Cui, Bin W. Zhang, and Nobuyuki Matubayasi. The Journal of Physical Chemistry B, 121(15), 3825-3841 (2017). DOI: 10.1021/acs.jpcb.6b12889.
Potts Hamiltonian models of protein co-variation, free energy landscapes, and evolutionary fitness.
Levy, Ronald M., Allan Haldane, and William F. Flynn. Current Opinion in Structural Biology, 43, 55-62 (2017). DOI: 10.1016/j.sbi.2016.11.004.
Inference of epistatic effects leading to entrenchment and drug resistance in HIV-1 protease.
Flynn, William F., Allan Haldane, Bruce E. Torbett, and Ronald M. Levy. Molecular Biology and Evolution, 34(6), 129 (2017). DOI: 10.1093/molbev/msx095.
Stratified UWHAM and Its Stochastic Approximation for Multicanonical Simulations Which are Far from Equilibrium.
Zhang, Bin W., Nanjie Deng, Zhiqiang Tan, and Ronald M. Levy. Journal of Chemical Theory and Computation, Web publication. (2017) DOI: 10.1021/acs.jctc.7b00651.
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)