B. A. 1970, Reed College Ph.D. 1976, Harvard University

Biological Chemistry; Physical Chemistry

We use a combination of computer simulations, statistical mechanics and modeling, to study the structure, function, folding, and dynamics of proteins in solution. Current research projects include problems in the statistical mechanics of solutions, protein folding and ligand binding, and protein dynamics on longer time scales. We are interested in the interplay between computational models and experiments at different levels of spatial and temporal resolution from atomic to mesoscopic, and from femtoseconds to seconds. We are also working with an interdisciplinary group of investigators to develop computational models for studying the interactions and evolution of HIV proteins and the mechanisms by which they acquire drug resistance.

Gallicchio, Emilio, Haoyuan Chen, He Chen, Michael Fitzgerald, Yang Gao, Peng He, Malathi Kalyanikar, Chuan Kao, Beidi Lu, Yijie Niu, Manasi Pethe, Jie Zhu, and Ronald M. Levy (2015). BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge. Journal of Computer-Aided Molecular Design, 29, 315-325.

Vijayan, R. S. K., Peng He, Vivek Modi, Krisna C. Duong-Ly, Haiching Ma, Jeffrey R. Peterson, Roland L. Dunbrack, and Ronald M. Levy (2015). Conformational Analysis of the DFG-Out Kinase Motif and Biochemical Profiling of Structurally Validated Type II Inhibitors. Journal of Medicinal Chemistry, 58, 466-479. PMCID: PMC4326797.

Deng, Nanjie, Stefano Forli, Peng He, Alex Perryman, Lauren Wickstrom, R. S. K. Vijayan, Theresa Tiefenbrunn, David Stout, Emilio Gallicchio, Arthur J. Olson, and Ronald M. Levy (2015). Distinguishing Binders from False Positives by Free Energy Calculations: Fragment Screening Against the Flap Site of HIV Protease. J. Phys. Chem. B, 119, 976-988. PMCID: PMC4306491.

Slaughter, Alison, Kellie A Jurado, Nanjie Deng, Lei Feng, Jacques J Kessl, Nikoloz Shkriabai, Ross C Larue, Hind J Fadel, Pratiq A Patel, Nivedita Jena, James R Fuchs, Eric Poeschla, Ronald M Levy, Alan Engelman, and Mamuka Kvaratskhelia (2014). The mechanism of H171T resistance reveals the importance of Nδ-protonated His171 for the binding of allosteric inhibitor BI-D to HIV-1 integrase. Retrovirology, 11. PMCID: PMC4251946.

Xia, Junchao and Ronald M. Levy (2014). Molecular Dynamics of the Proline Switch and Its Role in Crk Signaling. J. Phys. Chem. B, 118, 4535-4545. PMCID: PMC4007982.

Gallicchio, Emilio, Nanjie Deng, Peng He, Lauren Wickstrom, Alexander L. Perryman, Daniel N. Santiago, Stefano Forli, Arthur J. Olson, and Ronald M. Levy (2014). Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. Journal of Computer-Aided Molecular Design, 28, 475-490. PMCID: PMC4137862.

Deng, Nan-jie, Wei Dai, and Ronald M. Levy (2013). How Kinetics within the Unfolded State Affects Protein Folding: An Analysis Based on Markov State Models and an Ultra-Long MD Trajectory. J. Phys. Chem. B, 117, 12787-12799. PMCID: PMC3808496.

Yi, Guohua, Mauro Lapelosa, Rachel Bradley, Thomas M. Mariano, Denise Elsasser Dietz, Scott Hughes, Terri Wrin, Chris Petropoulos, Emilio Gallicchio, Ronald M. Levy, Eddy Arnold, and Gail Ferstandig Arnold (2013). Chimeric Rhinoviruses Displaying MPER Epitopes Elicit Anti-HIV Neutralizing Responses. None, 8, e72205. PMCID: PMC3765159.

Levy, Ronald M., Wei Dai, Nan-Jie Deng, and Dmitrii E. Makarov (2013). How long does it take to equilibrate the unfolded state of a protein?. Protein Science, 22, 1459-1465. PMCID: PMC3831662.

Wickstrom, Lauren, Peng He, Emilio Gallicchio, and Ronald M. Levy (2013). Large Scale Affinity Calculations of Cyclodextrin Host–Guest Complexes: Understanding the Role of Reorganization in the Molecular Recognition Process. J. Chem. Theory Comput., 9, 3136-3150. PMCID: PMC4137772.

Xia, Junchao, Nan-jie Deng, and Ronald M. Levy (2013). NMR Relaxation in Proteins with Fast Internal Motions and Slow Conformational Exchange: Model-Free Framework and Markov State Simulations. J. Phys. Chem. B, 117, 6625-6634. PMCID: PMC3727231.

Narayanan, Chitra, Daniel S. Weinstock, Kuen-Phon Wu, Jean Baum, and Ronald M. Levy (2012). Investigation of the Polymeric Properties of α-Synuclein and Comparison with NMR Experiments: A Replica Exchange Molecular Dynamics Study. J. Chem. Theory Comput., 8, 3929-3942. PMCID: PMC3496295.

Haq, Omar, Michael Andrec, Alexandre V. Morozov, and Ronald M. Levy (2012). Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease. PLoS Computational Biology, 8, e1002675. PMCID: PMC3435258.

Gallicchio, Emilio and Ronald M. Levy (2012). Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM). Journal of Computer-Aided Molecular Design, 26, 505-516. PMCID: PMC3383899.

Lapelosa, Mauro, Emilio Gallicchio, and Ronald M. Levy (2012). Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations. J. Chem. Theory Comput., 8, 47-60. PMCID: PMC3285237.

Wickstrom, Lauren, Emilio Gallicchio, and Ronald M. Levy (2012). The linear interaction energy method for the prediction of protein stability changes upon mutation. Proteins, 80, 111-125. PMCID: PMC3240711.

Tan, Zhiqiang, Emilio Gallicchio, Mauro Lapelosa, and Ronald M. Levy (2012). Theory of binless multi-state free energy estimation with applications to protein-ligand binding. J. Chem. Phys., 136, 144102. PMCID: PMC3339880.

Felts, Anthony K., Krystal LaBarge, Joseph D. Bauman, Dishaben V. Patel, Daniel M. Himmel, Eddy Arnold, Michael A. Parniak, and Ronald M. Levy (2011). Identification of Alternative Binding Sites for Inhibitors of HIV-1 Ribonuclease H Through Comparative Analysis of Virtual Enrichment Studies. Journal of Chemical Information and Modeling, 51, 1986-1998. PMCID: PMC3159817.

Deng, Nan-jie, Weihua Zheng, Emillio Gallicchio, and Ronald M. Levy (2011). Insights into the Dynamics of HIV-1 Protease: A Kinetic Network Model Constructed from Atomistic Simulations. J. Am. Chem. Soc., 133, 9387-9394. PMCID: PMC3116037.

Gallicchio, Emilio and Ronald M Levy (2011). Advances in all atom sampling methods for modeling protein–ligand binding affinities. Current Opinion in Structural Biology, 21, 161-166. PMCID: PMC3070828.