Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
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DOI：
10.1107/s0907444904026460
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发表时间：
2004-12-01
影响因子：
2.2
通讯作者：
Henrick, K
中科院分区：
文献类型：
--
作者：
Krissinel, E;Henrick, K
本文描述了蛋白质三维结构比较的SSM算法，它包括一种原始的基于蛋白质二级结构元素建立的图形匹配过程，然后是蛋白质主干C-α原子的迭代三维比对。将SSM结果与其他蛋白质比对服务器得到的结果进行了比较，并讨论了不同分数用于结构识别的优缺点。一个新的比分，平衡r.m.s.d。并提出了对齐长度N-ALIGN。研究发现，不同的服务器在新的分数上有相当好的一致性，但在r.m.s.d上表现出相当大的差异。和N向对齐。
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.