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Seq2Struct: a resource for establishing sequence-structure links.

Allegra Via1, Andreas Zanzoni, Manuela Helmer-Citterich

  • 1Department of Biology, Centre for Molecular Bioinformatics, University of Rome Tor Vergata 00133 Rome, Italy. seq2struct@cbm.bio.uniroma2.it

Bioinformatics (Oxford, England)
|September 30, 2004
PubMed
Summary
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Seq2Struct is a new web resource that identifies links between protein sequences and structures. It provides an extensive database of annotated links from major biological databases for researchers.

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Establishing links between protein sequences and structures is crucial for understanding protein function and evolution.
  • Existing methods often rely on database annotations or sequence alignment procedures.
  • A comprehensive and easily accessible resource for these links is needed.

Purpose of the Study:

  • To introduce Seq2Struct, a novel web resource for identifying sequence-structure links.
  • To provide an exhaustive collection of annotated links between protein sequence databases (Swiss-Prot + TrEMBL) and structure databases (Protein Data Bank + SCOP).

Main Methods:

  • Developed a relational database storing pre-established, highly reliable links between sequence and structure entries.
  • Enhanced the database with annotations from Swiss-Prot, Protein Data Bank (PDB), Structural Classification of Proteins (SCOP), Gene Ontology Annotation (GOA), and Database of Secondary Structure of Proteins (DSSP).

Related Experiment Videos

  • Created a WWW web interface for online querying and data download.

    • Main Results:

    • An extensive collection of annotated sequence-structure links is now available.
    • The Seq2Struct resource facilitates the identification of reliable cross-references between protein sequences and structures.
    • The database supports both online querying and data download.

    Conclusions:

    • Seq2Struct offers a valuable resource for researchers in bioinformatics and structural biology.
    • The integrated annotations enhance the utility of sequence-structure links.
    • The web-based accessibility promotes wider use and discovery in protein science.