February 15, Tue 2011
1:00 pm, MRB 100 Conference Room
Dr. Pengyu Ren
Department of Biomedical Engineering, The University of Texas at Austin
Molecular Modeling of Protein-Ligand Interactions
Molecular recognition between protein and ligand is essential for many biological processes and biomedical applications. Accurate prediction of protein-ligand binding thermodynamics with physics-based approaches requires realistic interatomic potential and sufficient sampling of configurational space. We have examined the possibility of using molecular dynamics simulations and the current-generation of force field in high throughput screening. Our benchmark on existing protein-ligand binding database yields encouraging results. While entropy evaluation remains a bottleneck, we have evidence that implicit-solvent based alchemical perturbation is promising. I will also discuss the recent development and application of a polarizable force field to protein-ligand binding, along with the potential and challenges we are facing.