Seq2Struct: a resource for establishing sequence-structure links

Bioinformatics. 2005 Feb 15;21(4):551-3. doi: 10.1093/bioinformatics/bti049. Epub 2004 Sep 28.

Abstract

Several methods for establishing cross-links between Protein Data Bank (PDB) structures or Structural Classification of Proteins (SCOP) domains and Swiss-Prot + TrEMBL sequences (or vice versa) rely on database annotations. Alternatively, sequence alignment procedures can be used. In this study, we describe Seq2Struct, a web resource for the identification of sequence-structure links. The resource consists of an exhaustive collection of annotated links between Swiss-Prot + TrEMBL and PDB + SCOP database entries. Links are based on pre-established highly reliable thresholds and stored in a relational database, which has been enhanced using annotations derived from Swiss-Prot, PDB, SCOP, GOA and DSSP databases. The Seq2Struct database contents, supported by a WWW web interface, can be queried both online and downloaded.

Availability: The Seq2Struct resource, with related documentation, is available at http://surface.bio.uniroma2.it/seq2struct/

Contact: seq2struct@cbm.bio.uniroma2.it.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Database Management Systems*
  • Databases, Protein*
  • Information Storage and Retrieval / methods*
  • Internet
  • Models, Chemical*
  • Models, Molecular
  • Proteins / analysis
  • Proteins / chemistry*
  • Proteins / metabolism
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*
  • Structure-Activity Relationship

Substances

  • Proteins