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Vol. 12, Issue 3, 503-514, March 2002

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

Daniel W.A. Buchan,1 Adrian J. Shepherd,1 David Lee,1,2 Frances M.G. Pearl,1 Stuart C.G. Rison,1 Janet M. Thornton,1,2 and Christine A. Orengo1,3

1 Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom; 2 Department of Crystallography, Birkbeck College, London, United Kingdom

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. Currently Gene3D 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.

3 Corresponding author.

12:503-514 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
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