Computationally predicting the oxidation of a protein

Jongwook Woo: Computer Information Systems Department, California State University, Los Angeles, California, USA. (TEL) +1-323-343-2916 (FAX) +1-323-343-5209 (E-Mail) jwoo5@calstatela.edu (URL) http://www.calstatela.edu/faculty/jwoo5

Abstract

If protein thiol groups are susceptible to oxidation, these protein groups will be easy to harm and cause diseases such as AIDS. We can predict the oxidation of protein thiol groups experimentally. Besides, we can predict the oxidation computationally in Bioinformatics because there are number of 3-D biological macromolecular structure data files given by many organizations. Assumed that Oxidation of protein thiol groups depends on percent solvent accessibility, the distance of thiolate stabilizing atoms from the sulfur atom, and the number of thiolate stabilizing atoms from the sulfur atom, the paper presents the computational algorithm and code that computes these three factors from protein data files in PDB (Protein Data bank) by RCSB. The objective is to predict the oxidation of a protein computationally at high accuracy, especially for PDB files in protein-DNA complex.

Short Biography

Jongwook Woo: Jongwook Woo is an Assistant Professor in the Computer Information Systems Department at California State University. His current research interests are in e-Business, m-Commerce, Bioinformatics, Distributed and Parallel Computing, and Internet Protocol.

Before he joined the faculty of California State University in 2002, he was a Research Professor at Yonsei University in 2002. He received a BS and a MS degree from the Department of Electronic Engineering, Yonsei University, in 1989 and 1991 respectively; an MS degree from the Department of Computer Science, University of Southern California (USC), in 1998; and a Ph.D degree in Computer Engineering from University of Southern California (USC), in 2001.