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.
Via, A., Zanzoni, A., HELMER CITTERICH, M. (2005). Seq2Struct: a resource for establishing sequence-structure links. BIOINFORMATICS, 21(4), 551-553 [10.1093/bioinformatics/bti049].
Seq2Struct: a resource for establishing sequence-structure links
HELMER CITTERICH, MANUELA
2005-02-15
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.| File | Dimensione | Formato | |
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