BME PhD Prospectus Defense – Bing Xia

4:00 pm on Friday, July 11, 2014
44 Cummington Mall, Room 203
Title: Flexible Macromolecular Docking With Experimental Restraints

Dr. Sandor Vajda (Research Advisor, Chair)
Dr. Dima Kozakov
Dr. Yannis Paschalidis
Dr. Karen Allen

Protein interactions play a central role in the functioning of living cells. While there are now more than 100,000 structures in the Protein Data Bank, structures of protein complexes remain relatively scarce. Predicting the structure of protein-protein complexes and protein-small molecule complexes using computational methods is a valuable tool when experimental structures are unavailable, and these techniques are also useful for computational drug discovery. Our lab has developed a multistage approach to macromolecular docking, which consists of a global search for low energy conformations of a receptor and ligand followed by stages of refinement. The goal of this project is to apply experimental restraints to different stages of the docking process, as well as to enable sidechain flexibility during the docking process.