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

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 atoms. The S...

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Bibliographic Details
Published in:Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2004-12, Vol.60 (12-1), p.2256-2268
Main Authors: Krissinel, E., Henrick, K.
Format: Article
Language:English
Subjects:
Algorithms
Internet
Models, Molecular
Protein Conformation
Protein Structure, Secondary
Proteins - chemistry
Quality Control
secondary-structure matching (SSM)
Software
three-dimensional protein structure comparison
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Summary: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 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 , 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 .
ISSN:1399-0047
0907-4449
1399-0047
DOI:10.1107/S0907444904026460