Seq2Struct: a resource for establishing sequence-structure links | Zendy

Allegra Via | Zendy; Andreas Zanzoni | Zendy; Manuela HelmerCitterich | Zendy

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Seq2Struct: a resource for establishing sequence-structure links

Author(s) -

Allegra Via,

Andreas Zanzoni,

Manuela HelmerCitterich

Publication year - 2004

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bti049

Subject(s) - protein data bank (rcsb pdb) , uniprot , protein data bank , computer science , documentation , sequence database , resource (disambiguation) , structural classification of proteins database , database , relational database , information retrieval , protein structure , biology , computer network , biochemistry , gene , programming language

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.

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