Three-Dimensional Motif Search of Proteins Using Abstract Representation of Secondary Structure Segment

Hiroaki KATO (
Yoshimasa TAKAHASHI (

Laboratory for Molecular Information Systems,
Department of Knowledge-based Information Engineering,
Toyohashi University of Technology, Tempaku, Toyohashi 441 JAPAN


This paper describes an approach to three-dimensional (3-D) motif search of proteins, which is based on a graph-theoretical clique finding algorithm. In this implementation, higher abstract representation of a protein structure has been also investigated for the description of secondary structure information such as alpha-helix and beta-strand. The algorithms and the implementations are discussed with a couple of execution examples of the 3-D motif search using protein structure database.