Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

被引：3293

作者：

Krissinel, E ^{[1
]}

Henrick, K ^{[1
]}

机构：

[1] European Bioinformat Inst, Cambridge CB10 1SD, England

来源：

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY | 2004年 / 60卷

关键词：

D O I：

10.1107/S0907444904026460

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The present paper describes the SSM algorithm of protein structure comparison in three dimensions, which includes an original procedure of matching graphs built on the protein's secondary-structure elements, followed by an iterative three-dimensional alignment of protein backbone C-alpha atoms. The SSM results are compared with those obtained from other protein comparison servers, and the advantages and disadvantages of different scores that are used for structure recognition are discussed. A new score, balancing the r.m.s.d. and alignment length N-align, is proposed. It is found that different servers agree reasonably well on the new score, while showing considerable differences in r.m.s.d. and N-align.

引用

页码：2256 / 2268

页数：13

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