Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (702K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (16)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Buchan, D. W. A.
Right arrow Articles by Orengo, C. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Buchan, D. W. A.
Right arrow Articles by Orengo, C. A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Phil Trans R Soc BHome page
K. Fleming, L. A Kelley, S. A Islam, R. M MacCallum, A. Muller, F. Pazos, and M. J.E Sternberg
The proteome: structure, function and evolution
Phil Trans R Soc B, March 29, 2006; 361(1467): 441 - 451.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
O. Krishnadev, N. Rekha, S. B. Pandit, S. Abhiman, S. Mohanty, L. S. Swapna, S. Gore, and N. Srinivasan
PRODOC: a resource for the comparison of tethered protein domain architectures with in-built information on remotely related domain families
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W126 - W129.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Liu and B. Rost
Sequence-based prediction of protein domains
Nucleic Acids Res., July 7, 2004; 32(12): 3522 - 3530.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. J. McGuffin, S. A. Street, K. Bryson, S.-A. Sorensen, and D. T. Jones
The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms
Nucleic Acids Res., January 1, 2004; 32(90001): D196 - 199.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Fleming, A. Muller, R. M. MacCallum, and M. J. E. Sternberg
3D-GENOMICS: a database to compare structural and functional annotations of proteins between sequenced genomes
Nucleic Acids Res., January 1, 2004; 32(90001): D245 - 250.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. Hershkovitz, E. Tannenbaum, S. B. Howerton, A. Sheth, A. Tannenbaum, and L. D. Williams
Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA
Nucleic Acids Res., November 1, 2003; 31(21): 6249 - 6257.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.