Searching for patterns of amino acids in 3D protein structures
Searching for patterns of amino acids in 3D protein structures
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DOI：
10.1021/ci0255984
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发表时间：
2003-03-01
期刊：
影响因子：
--
通讯作者：
Willett, P
中科院分区：
文献类型：
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作者：
Spriggs, RV;Artymiuk, PJ;Willett, P
本文介绍了在蛋白质数据库中搜索三维结构中氨基酸侧链模式的程序ASSAM。Assam通过从主链向氨基酸功能部分绘制的矢量来表示氨基酸，然后计算蛋白质的图形表示，其中各个侧链矢量是节点，矢量间距离是边。然后，可以借助子图同构算法来搜索蛋白质数据库结构中查询模式的存在。最近对ASSAM的增强允许搜索包括以下内容：除侧链之外的主链结构；侧链的二级结构和溶剂可及性；与已知结合位点的允许距离；二硫键；以及改进的通用查询和通配符查询。通过对蛋白质数据库中典型3D查询模式的广泛搜索，证明了这些方法的有效性。
This paper describes the program ASSAM, which has been developed to search for patterns of amino acid side-chains in the 3D structures in the Protein Data Bank. ASSAM represents an amino acid by a vector drawn from the main chain towards the functional part of the amino acid and then computes a graph representation of a protein in which the individual side-chain vectors are the nodes and the intervector distances are the edges. The presence of a query pattern in a Protein Data Bank structure can then be searched for by means of a subgraph isomorphism algorithm. Recent enhancements to ASSAM allow searches to include the following: the main-chain structure in addition to the side-chains; the secondary structure and solvent accessibility of side-chains; allowable distances from a known binding-site; disulfide bridges; and improved generic and wild-card queries. The effectiveness of these approaches is demonstrated by extensive searches of the Protein Data Bank for typical 3D query patterns.