|Office:||Wright Rieman Labs A205|
|Mail:||BioMaPS Institute for Quantitative Biology, 610 Taylor Road, Piscataway, NJ 08854|
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. Together with a group of investigators with complementary expertise in molecular biology, statistical physics, control theory, and computer science, we are working to develop computational models for complex biological systems involved in the regulation of gene expression.
Awards & Honors
- A. P. Sloan Foundation Fellow (1982-84)
- National Institutes of Health Research Career Development Award (1982-86)
- National Institutes of Health Fogarty Fellow (1986)
- John Simon Guggenheim Foundation Fellow (1995-96)
- Rutgers University Board of Trustees Award for Excellence in Research (1996)
- Japan Society for the Promotion of Science Fellowship (1996)
- AAAS, Fellow (1998)
- Board of Governors Professor of Chemistry (2002)
Ravindranathan, K.P., E. Gallicchio, R.A. Friesner, A.E. McDermott, and R.M. Levy. Conformational Equilibrium of Cytochrome P450 BM-3 Complexed with N-Palmitoylglycine: A Replica Exchange Molecular Dynamics Study. J. Am. Chem. Soc., 128, 5786-5791 (2006).
Su, Y., E. Gallicchio, K. Das, E. Arnold, and R.M. Levy. Linear Interaction Energy (LIE) Models for Ligand Binding in Implicit Solvent: Theory and Application to the Binding of NNRTIs to HIV-1 Reverse Transcriptase. J. Chem. Theory Comput., 3, 256-277 (2007).
Ravindranathan, K.P., E. Gallicchio, A.E. McDermott, and R.M. Levy. Conformational dynamics of substrate in the active site of cytochrome P450 BM-3/NPG complex: Insights from NMR order parameters. J. Am. Chem. Soc., 129, 474-475 (2007).
Weinstock, D.S., C. Narayanan, A.K. Felts., M. Andrec, R.M. Levy, K-P. Wu., and J. Baum. Distinguishing Among Structural Ensembles of the GB1 Peptide: REMD Simulations and NMR Experiments. J. Am. Chem. Soc., 129, 4858-4859 (2007).
Felts, A.K., E. Gallicchio, D. Chekmarev, K.A. Paris, R.A. Friesner, and R.M. Levy. Prediction of Protein Loop Conformations Using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. J. Chem. Theor. Comput., 4, 855-868 (2008).
Knight, J.L., Z. Zhou, E. Gallicchio, D.M. Himmel, R.A. Friesner, E. Arnold, and R.M. Levy. Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion angle sampling, Acta. Cryst., D64, 383-396 (2008).
Zhou, Z., A.K. Felts, R.A. Friesner, and R.M. Levy. Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets. J. Chem. Inf. Model., 47, 1599-1608 (2007).
Zheng, W., M. Andrec, E. Gallicchio, and R.M. Levy. Simulating replica exchange simulations of protein folding with a kinetic network model. Proc. Natl. Acad. Sci. USA, 104, 15340-15345 (2007).
Gallicchio, E., R.M. Levy, and M. Parashar. Asynchronous Replica Exchange for Molecular Simulations. J. Comput. Chem., 29, 788-794 (2008).
Zheng, W., M. Andrec, E. Gallicchio, and R.M. Levy. Simple Continuous and Discrete Models for Simulating Replica Exchange Simulations of Protein Folding. J. Phys. Chem. B, 112, 6083-6093 (2008).
Lapelosa, M., E. Gallicchio, G. Ferstandig Arnold, E. Arnold, and R.M. Levy. In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes. J. Mol. Biol., 385, 675-691 (2009).