TOPS: an enhanced database of protein structural topology

被引:79
作者
Michalopoulos, I
Torrance, GM
Gilbert, DR
Westhead, DR [1 ]
机构
[1] Univ Leeds, Sch Biochem & Mol Biol, Leeds LS2 9JT, W Yorkshire, England
[2] Univ Glasgow, Dept Comp Sci, Glasgow G12 8QQ, Lanark, Scotland
关键词
D O I
10.1093/nar/gkh060
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The TOPS database holds topological descriptions of protein structures. These compact and highly abstract descriptions reduce the protein fold to a sequence of Secondary Structure Elements (SSEs) and three sets of pairwise relationships between them, hydrogen bonds relating parallel and anti-parallel beta strands, spatial adjacencies relating neighbouring SSEs, and the chiralities of selected supersecondary structures, including connections in betaalphabeta units and between parallel alpha helices. The database is used as a resource for visualizing folding topologies, fast topological pattern searching and structure comparison. Here, significant enhancements to the TOPS database are described. The topological description has been enhanced to include packing relationships between helices, which significantly improves the description of protein folds with little beta strand content. Further, the topological description has been annotated with sequence information. The query interfaces to the database have been improved and the new version can be found at http://www.tops.leeds.ac.uk/.
引用
收藏
页码:D251 / D254
页数:4
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