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Bioinformatics Advance Access originally published online on September 28, 2004
Bioinformatics 2005 21(4):551-553; doi:10.1093/bioinformatics/bti049
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Bioinformatics vol. 21 issue 4 © Oxford University Press 2005; all rights reserved.

Seq2Struct: a resource for establishing sequence-structure links

Allegra Via *, Andreas Zanzoni and Manuela Helmer-Citterich

Department of Biology, Centre for Molecular Bioinformatics, University of Rome Tor Vergata 00133 Rome, Italy

*To whom correspondence should be addressed.

Summary: 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{at}cbm.bio.uniroma2.it


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Home page
 Nucleic Acids ResHome page
A. Zanzoni, G. Ausiello, A. Via, P. F. Gherardini, and M. Helmer-Citterich
Phospho3D: a database of three-dimensional structures of protein phosphorylation sites
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D229 - D231.
[Abstract] [Full Text] [PDF]


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