Skip Navigation

Nucleic Acids Research 2006 34(Database Issue):D281-D284; doi:10.1093/nar/gkj057
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (71K) Freely available
Right arrow Screen PDF (75K) 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 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 Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Yeats, C.
Right arrow Articles by Orengo, C. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yeats, C.
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, 2006, Vol. 34, Database issue D281-D284
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Gene3D: modelling protein structure, function and evolution

Corin Yeats*, Michael Maibaum, Russell Marsden, Mark Dibley, David Lee, Sarah Addou and Christine A. Orengo

Department of Biochemistry and Molecular Biology, University College London Gower Street, London, WC1E 6BT, UK

*To whom correspondence should be addressed. Tel: +44 20 7679 3890; Fax: +44 20 7679 7193; Email: yeats{at}biochem.ucl.ac.uk

Received September 15, 2005. Accepted October 4, 2005.

The Gene3D release 4 database and web portal (http://cathwww.biochem.ucl.ac.uk:8080/Gene3D) provide a combined structural, functional and evolutionary view of the protein world. It is focussed on providing structural annotation for protein sequences without structural representatives—including the complete proteome sets of over 240 different species. The protein sequences have also been clustered into whole-chain families so as to aid functional prediction. The structural annotation is generated using HMM models based on the CATH domain families; CATH is a repository for manually deduced protein domains. Amongst the changes from the last publication are: the addition of over 100 genomes and the UniProt sequence database, domain data from Pfam, metabolic pathway and functional data from COGs, KEGG and GO, and protein–protein interaction data from MINT and BIND. The website has been rebuilt to allow more sophisticated querying and the data returned is presented in a clearer format with greater functionality. Furthermore, all data can be downloaded in a simple XML format, allowing users to carry out complex investigations at their own computers.

The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors


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
 Nucleic Acids ResHome page
D. Wilson, R. Pethica, Y. Zhou, C. Talbot, C. Vogel, M. Madera, C. Chothia, and J. Gough
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D380 - D386.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
R. D. Finn, J. W. Stalker, D. K. Jackson, E. Kulesha, J. Clements, and R. Pettett
ProServer: a simple, extensible Perl DAS server
Bioinformatics, June 15, 2007; 23(12): 1568 - 1570.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. J. Mulder, R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, D. Binns, P. Bork, V. Buillard, L. Cerutti, R. Copley, et al.
New developments in the InterPro database
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D224 - D228.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Wilson, M. Madera, C. Vogel, C. Chothia, and J. Gough
The SUPERFAMILY database in 2007: families and functions
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D308 - D313.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
G. A. Reeves, J. M. Thornton, and the BioSapiens Network of Excellence
Integrating biological data through the genome
Hum. Mol. Genet., April 15, 2006; 15(suppl_1): R81 - R87.
[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.