College of Liberal Arts & Sciences

Molecular Modeling of Protein-Ligand Interactions

Tuesday, February 15, 2011

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.

One of 34 U.S. public institutions in the prestigious Association of American Universities
44 nationally ranked graduate programs.
—U.S. News & World Report
Top 50 nationwide for size of library collection.
23rd nationwide for service to veterans —"Best for Vets," Military Times
KU Today