Pengyu Ren


Our research integrates high-performance computing with chemistry and physics to address biological and medical challenges from single molecules to the genome. Specific areas of research include protein-ligand interactions for drug discovery, RNA structure prediction and biomaterials design. In collaboration with other experimental groups, we utilize computer modeling and simulations to understand these complex biomolecular systems and to discover molecules for treating disease and improving human health.

Protein-ligand interactions: We are interested in developing and applying physical models and computational algorithms to predict the specific interaction between protein and small drug-like molecules. Currently, we are investigating a series of computational models base on a polarizable atomic multipole potential energy function (AMOEBA). Our goal is to achieve chemical accuracy in the prediction and to better our understanding of the physical principles of molecular recognition and interactions. Protein targets of interest include various proteases and kinases.


Correlation of RNA Secondary Structure Statistics with Thermodynamic Stability and Applications to Folding, J. C. Wu, D. P. Gardner, S. Ozer, R. R. Gutell and PY Ren, J. Mol. Biol. (2009) 391, 769-783

Calculation of Protein-Ligand Binding Free Energy Using a Polarizable Potential, D. Jiao, P.A. Golubkov, T. Darden, P. Ren, Proc. Natl. Acad. Sci. USA 105 (17): 6290 (2008)

Molecular Modeling of Conformational Properties of Oligodepsipeptides, J. Zhang, M. King, L. Suggs, and P. Ren, Biomacromolecules, 8, 3015-3024 (2007)