Gene3D: Structural Assignment for Whole Genes and Genomes Using the CATH Domain Structure Database

  1. Daniel W.A. Buchan1,
  2. Adrian J. Shepherd1,
  3. David Lee1,2,
  4. Frances M.G. Pearl1,
  5. Stuart C.G. Rison1,
  6. Janet M. Thornton1,2, and
  7. Christine A. Orengo1,3
  1. 1Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom; 2Department of Crystallography, Birkbeck College, London, United Kingdom

Abstract

We present a novel web-based resource,Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. CurrentlyGene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies.

Footnotes

  • 3 Corresponding author.

  • E-MAIL orengo{at}biochem.ucl.ac.uk; FAX 44-207-7679-7193.

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.213802.

    • Received September 5, 2001.
    • Accepted January 11, 2002.
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