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© Oxford University Press

SS3D-P2: a three-dimensional substructure search program for protein motifs based on secondary structure elements

Hiroaki Kato and Yoshimasa Takahashi 1

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

1To whom correspondence should be addressed

This paper discusses the implementation of a three-dimensional (3D) structure motif search of proteins. Each protein structure is represented by a set of secondaiy structure elements (SSEs) which involves {alpha}-helix segments and ß-strand segments. In describing it, every SSE is further reduced into a two-node graph that consists of the starting amino acid residue, the ending residue and a pseudo-bond between them. The searching algorithm is based on a graph theoretical clique-finding algorithm that has been used for 3D substructure searching in small organic molecules. The program SS3D-P2 was validated using proteins that have well-known 3D motifs, and it correctly found the Greek key motif within an eye lens protein, crystallin that consists of four anti-parallel ß strands. The program was also successfully applied to searching for the more complex 3D motif TIM-type ß-harrel motif, with a protein structure database from the Protein Data Bank.

CONTACT:: E-mail: {hiro,raka}{at}mis.tutkie.tut.ac.jp

Received on April 30, 1997; accepted on July 2, 1997

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