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PubMed · 16381865

Gene3D: modelling protein structure, function and evolution.

Corin Yeats·Michael Maibaum·Russell Marsden·Mark Dibley·David Lee·Sarah Addou·Christine A Orengo
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Abstract

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.

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Databases, ProteinEvolution, MolecularGenomicsInternetModels, MolecularProtein Structure, TertiaryProteinsProteomeSequence Analysis, ProteinUser-Computer InterfaceJournal ArticleResearch Support, Non-U.S. Gov't

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Corin Yeats, Michael Maibaum, Russell Marsden, Mark Dibley, David Lee, Sarah Addou, Christine A Orengo. 2006-01-01. Gene3D: modelling protein structure, function and evolution.. https://doi.org/10.1093/nar%2Fgkj057

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