Poster Sessions

BIOINFO-9

Chin-Hsien Tai

C. H. Tai, J. F. Gibrat, J. Garnier, P. J. Munson, B. K. Lee

Parsing Protein Structures into Domains by Using Recurrence

Domains are basic units of protein structure and essential for exploring protein fold space and structure evolution. With structural genomics initiative, the number of protein structures in PDB is increasing dramatically and domain parsing needs to be done automatically. Most of the existing structural domain parsing programs consider the compactness of the domains and/or the number and strength of internal (intra-domain) and external (inter-domain) contacts. Here we present a completely different approach. Taking advantage of the growing number of known structures in the PDB, the chains are parsed solely by using recurrence of similar structures that appear in the database. One against all structure comparisons were performed by VAST. Then the VAST cliques were collected and clustered using mathematical procedures akin to those used for analyzing the microarray data. These clusters define domains. NDO scores were used to compare the results with SCOP and CATH domain boundaries as well as with those from other programs. Our algorithm gave results that are comparable to those of several existing programs. It handles segmented domains as well as non-segmented domains. Analyzing the cliques contributed by other structures should contain the evolutionary information.