Open AccessSecondary‐structure matching (SSM), a new tool for fast protein structure alignment in three dimensions
Author(s) -
Krissinel E.,
Henrick K.
Publication year - 2004
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444904026460
Subject(s) - matching (statistics) , server , computer science , algorithm , structural alignment , protein secondary structure , protein structure , mathematics , sequence alignment , statistics , biology , world wide web , biochemistry , peptide sequence , gene
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 .