A computer system to perform structure comparison using TOPS representations of protein structure

被引：26

作者：

Gilbert, D ^{[1
]}

Westhead, D

Viksna, J

Thornton, J

机构：

[1] City Univ London, Dept Comp, London EC1V 0HB, England

[2] European Inst Bioinformat, Cambridge, England

[3] Univ Leeds, Sch Biochem & Mol Biol, Leeds LS2, W Yorkshire, England

[4] Univ Latvia, Inst Math & Comp Sci, LV-1459 Riga, Latvia

[5] UCL, Dept Biochem, London WC1E 6BT, England

[6] Univ London Birkbeck Coll, Dept Crystallog, London WC1E 7HX, England

来源：

COMPUTERS & CHEMISTRY | 2001年 / 26卷 / 01期

基金：

英国工程与自然科学研究理事会;

关键词：

structure comparison; constraints; pattern matching; pattern discovery; protein motifs; protein topology;

D O I：

10.1016/S0097-8485(01)00096-1

中图分类号：

O6 [化学];

学科分类号：

0703 ;

摘要：

We describe the design and implementation of a fast topology-based method for protein structure comparison. The approach uses the TOPS topological representation of protein structure, aligning two structures using a common discovered pattern and generating measure of distance derived from an insert score. Heavy use is made of a constraint-based pattern-matching algorithm for TOPS diagrams that we have designed and described elsewhere (Bioinformatics 15(4) (1999) 317). The comparison system is maintained at the European Bioinformatics Institute and is available over the Web at tops.ebi.ac.uktops. Users submit a structure description in Protein Data Bank (PDB) format and can compare it with structures in the entire PDB or a representative subset of protein domains, receiving the results by email. (C) 2001 Elsevier Science Ltd. All rights reserved.

引用

页码：23 / 30

页数：8

共 24 条

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