Journal
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
Volume 60, Issue -, Pages 2256-2268Publisher
INT UNION CRYSTALLOGRAPHY
DOI: 10.1107/S0907444904026460
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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.
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