Blog
About

84
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

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

      Acta Crystallographica Section D: Biological Crystallography

      Software, Quality Control, chemistry, Proteins, Protein Structure, Secondary, Protein Conformation, Models, Molecular, Internet, Algorithms

      Read this article at

      ScienceOpenPublisherPubMed
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          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.

          Related collections

          Author and article information

          Journal
          10.1107/S0907444904026460
          15572779

          Comments

          Comment on this article