Kato H, Takahashi Y
Department of Knowledge-based Information Engineering, Toyohashi University of Technology, Japan. ¿hiro,taka¿@mis.tutkie.tut.ac.jp
Comput Appl Biosci. 1997 Dec;13(6):593-600. doi: 10.1093/bioinformatics/13.6.593.
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 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 beta strands. The program was also successfully applied to searching for the more complex 3D motif, TIM-type beta-barrel motif, with a protein structure database from the Protein Data Bank.
本文讨论了蛋白质三维（3D）结构基序搜索的实现。每个蛋白质结构由一组二级结构元件（SSE）表示，其中包括α-螺旋段和β-链段。在描述时，每个SSE进一步简化为一个双节点图，该图由起始氨基酸残基、终止残基以及它们之间的一个伪键组成。搜索算法基于一种图论团簇查找算法，该算法已用于小分子的3D子结构搜索。程序SS3D-P2使用具有已知3D基序的蛋白质进行了验证，并且它在一种晶状体蛋白（晶状体球蛋白）中正确地找到了由四条反平行β链组成的希腊钥匙基序。该程序还成功地应用于从蛋白质数据库中搜索更复杂的3D基序——TIM型β桶基序。
