Gene3D: modelling protein structure, function and evolution.
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.
Yeats
Corin
C
Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK. yeats@biochem.ucl.ac.uk
Maibaum
Michael
M
Marsden
Russell
R
Dibley
Mark
M
Lee
David
D
Addou
Sarah
S
Orengo
Christine A
CA
D030562:Databases, Protein; D019143:Evolution, Molecular; D023281:Genomics; D020407:Internet; D008958:Models, Molecular; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry* / Q000235:genetics* / Q000502:physiology; D020543:Proteome / Q000737:chemistry; D020539:Sequence Analysis, Protein; D014584:User-Computer Interface
D011506:Proteins; D020543:Proteome