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Bioinformatics Advance Access published online on September 28, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti049
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 18, 2004
Revised September 22, 2004
Accepted September 22, 2004

Applications note

Seq2Struct: a resource for establishing sequence-structure links

Allegra Via 1*, Andreas Zanzoni 1, and Manuela Helmer-Citterich 1

1 Centre for Molecular Bioinformatics, Dept. of Biology, University of Rome Tor Vergata, 00133 Rome, Italy

* To whom correspondence should be addressed. E-mail: allegra{at}cbm.bio.uniroma2.it.


  Abstract

Summary: Several methods for establishing cross-links between PDB structures or SCOP domains and Swiss-Prot + TrEMBL sequences (or vice versa) rely on databases annotations. Alternatively, sequence alignment procedures can be used. In this report, 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 with annotation derived from Swiss-Prot, PDB, SCOP, GOA and DSSP databases. The Seq2Struct database contents, supported by a WWW web interface, can be both queried on line and downloaded.

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


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Home page
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A. Zanzoni, G. Ausiello, A. Via, P. F. Gherardini, and M. Helmer-Citterich
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[Abstract] [Full Text] [PDF]


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