This summer I will be working with Brian Chen, a Ph.D. student at Rice University, and Dr. Lydia Kavraki to help test a program that compares protein structures in a effort to determine a protein's function. I have been given several goals for the summer. The first few weeks will be spent on research. I need to learn about a protein's structure and how that relates to its function. To help familiarize myself with protein structures, I will use Rasmol, protein visualization software, and GeoHash, Brian's protein comparison software. I also need to read about Evolutionary Trace and Geometric Hashing, the two major algorithms utilized by Brian in GeoHash. Once these goals have been completed I am to test Brian's program with two major goals in mind.
Goal 1: To tune his methods to work faster and more reilably, and offer suggestions on improvements and changes to make to GeoHash