Automated Identification of Three-Dimensional Motif in Proteins

Hiroaki Kato (hiro@mis.tutkie.tut.ac.jp)
Yoshimasa Takahashi (taka@mis.tutkie.tut.ac.jp)

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 automated identification of three-dimensional (3-D) motif in proteins. Here, the structure of a protein was reduced into abstract representation which consists of the alpha-helix and beta-strand secondary structure elements, these being described by vectors in 3-D space rather than the point-like atoms that are used in the simple Calpha approximation. The algorithms and the implementations are discussed with a couple of execution examples of the identification of the 3-D motif candidates using well known motifs.