Susan Lin
Nancy Amato, advisor

Department of Computer Science
Texas A&M University
College Station, TX 77843

The goal of this project is to use OBPRM (obstacle based probablistic roadmap) methods to study protein folding. Given a starting (denatured) configuration and a goal (antive fold) configuration, we are able to construct a road map and derive a set of possible paths for the protein to follow. To do so, we model proteins as multi-link tree-like robots with many degrees of freedom. Our current work concentrates on secondary structure formation order. We are interested in exploring formation order as a way to validate our work. Other studies on protein folding behavior indicate that the formation of secondary structure (alpha-helices and beta-sheets) is not absolute -- the same protein may exhibit different folding patters under the same conditions. Thus far our results agree with these findings. Our future work will be directed towards making our methods more accurate, and to generate better energy landscapes.