Secondary-structure Matching (SSM), a New Tool for Fast Protein Structure Alignment in Three Dimensions

Overview

Journal Acta Crystallogr D Biol Crystallogr

Specialty Chemistry

Date 2004 Dec 2

PMID 15572779

Citations 2067

Authors

E Krissinel

K Henrick

Affiliations

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Abstract

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 Calpha 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 Nalign, 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 Nalign.

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