Paper Info
Title
SS3D-P2: a three dimensional substructure search program for protein motifs based on secondary structure elements.
Abstract
This paper-discusses the implementation of a three-dimensional (3D) structure motif search of proteins. Each protein structure is represented by a set of secondary structure elements (SSEs) which involves alpha-helix segments and beta-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 seal-ching algorithm is based on a graph theoretical clique-finding algorithm that has been used for 30 substructure searching in small organic molecules. The program SS3D-P2 was validated using proteins that have well-known 30 motifs, and it correctly found the Greek key motif within an eye lens protein, crystallin, that consists of four anti-parallel beta strands. The program was also successfully applied to searching for the more complex 30 motif, TIM-type beta-barrel motif, with a protein structure database from the Protein Data Bank. Contact: E-mail: {hiro, taka}@mis.tutkie.tut.ac.jp.
Year
DOI
Venue
1997
10.1093/bioinformatics/13.6.593
COMPUTER APPLICATIONS IN THE BIOSCIENCES
Keywords
DocType
Volume
protein motif,tertiary structure,structural unit,secondary structure,three dimensional
Journal
13
Issue
ISSN
Citations 
6
0266-7061
3
PageRank 
References 
Authors
0.77
0
2
Name
Order
Citations
PageRank
Hiroaki Kato13718.25
Yoshimasa Takahashi215215.90