Integrated search and alignment of protein structures

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Sacan A., TOROSLU İ. H., Ferhatosmanoglu H.

BIOINFORMATICS, vol.24, no.24, pp.2872-2879, 2008 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 24 Issue: 24
  • Publication Date: 2008
  • Doi Number: 10.1093/bioinformatics/btn545
  • Journal Name: BIOINFORMATICS
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Page Numbers: pp.2872-2879
  • Middle East Technical University Affiliated: Yes

Abstract

Motivation: Identification and comparison of similar three-dimensional (3D) protein structures has become an even greater challenge in the face of the rapidly growing structure databases. Here, we introduce Vorometric, a new method that provides efficient search and alignment of a query protein against a database of protein structures. Voronoi contacts of the protein residues are enriched with the secondary structure information and a metric substitution matrix is developed to allow efficient indexing. The contact hits obtained from a distance-based indexing method are extended to obtain high-scoring segment pairs, which are then used to generate structural alignments.