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Nucleic Acids Research, 2003, Vol. 31, No. 1 469-473
© 2003 Oxford University Press

Gene3D: structural assignments for the biologist and bioinformaticist alike

Daniel W. A. Buchan1, Stuart C. G. Rison1, James E. Bray1, David Lee1,2, Frances Pearl1, Janet M. Thornton1,3 and Christine A. Orengo*,1

1 Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK 2 Department of Crystallography, Birkbeck College, Malet Street, Bloomsbury, London WC1E 7HX, UK 3 EMBL—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

*To whom correspondence should be addressed. Tel: +44 2076797193; Email: c.orengo{at}ucl.ac.uk
Present address: Stuart C. G. Rison, Royal Vetinary College, Department of Pathology and Infectious Diseases, Royal College Street, London NW1 0TU
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

ABSTRACT

The Gene3D database (http://www.biochem.ucl.ac.uk/bsm/cath_new/Gene3D/) provides structural assignments for genes within complete genomes. These are available via the internet from either the World Wide Web or FTP. Assignments are made using PSI-BLAST and subsequently processed using the DRange protocol. The DRange protocol is an empirically benchmarked method for assessing the validity of structural assignments made using sequence searching methods where appropriate assignment statistics are collected and made available. Gene3D links assignments to their appropriate entries in relevent structural and classification resources (PDBsum, CATH database and the Dictionary of Homologous Superfamilies). Release 2.0 of Gene3D includes 62 genomes, 2 eukaryotes, 10 archaea and 40 bacteria. Currently, structural assignments can be made for between 30 and 40 percent of any given genome. In any genome, around half of those genes assigned a structural domain are assigned a single domain and the other half of the genes are assigned multiple structural domains. Gene3D is linked to the CATH database and is updated with each new update of CATH.


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