Topic: "Protein structure prediction and design via rotamer libraries"

Mr. Wei Xie is a doctoral candidate under the supervision of Professor Nikolaos V. Sahinidis in the Department of Chemical and Biomolecular Engineering at the University of Illinois at Urbana-Champaign.  His research interests are in computational biology.

Abstract:  Protein structure prediction and design are fundamental problems in the understanding of life and drug design.  Solution of these problems requires sophisticated computational techniques.  Methods based on rotamer libraries have been recently applied to these problems with very encouraging results.  This talk will begin with a tutorial on prediction of protein structures through homologs, conformational analysis of protein side chains, and rotamer libraries.  We will next review several mathematical formulations for library-based approaches, computational complexity results, and algorithms. The emphasis will be on the various Dead-End-Elimination and Bounding Elimination criteria, which have, by far, been the most successful methods.  In the last part of this talk, we will present some of our results, including the tightness of a Linear-Programming-based lower bound, a Benders decomposition to solve very large-scale Linear Programming relaxations, and a new elimination criterion based on reduced costs that are computed via a combinatorial algorithm.