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    Gene3D: comprehensive structural and functional annotation of genomes

    Yeats, C. and Lees, J. and Reid, A. and Kellam, P. and Martin, Nigel and Liu, X. and Orengo, C.A. (2008) Gene3D: comprehensive structural and functional annotation of genomes. Nucleic Acids Research 36 (S1), D414-D418. ISSN 0305-1048.

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    Abstract

    Gene3D provides comprehensive structural and functional annotation of most available protein sequences, including the UniProt, RefSeq and Integr8 resources. The main structural annotation is generated through scanning these sequences against the CATH structural domain database profile-HMM library. CATH is a database of manually derived PDB-based structural domains, placed within a hierarchy reflecting topology, homology and conservation and is able to infer more ancient and divergent homology relationships than sequence-based approaches. This data is supplemented with Pfam-A, other non-domain structural predictions (i.e. coiled coils) and experimental data from UniProt. In order to enhance the investigations possible with this data, we have also incorporated a variety of protein annotation resources, including protein–protein interaction data, GO functional assignments, KEGG pathways, FUNCAT functional descriptions and links to microarray expression data. All of this data can be accessed through a newly re-designed website that has a focus on flexibility and clarity, with searches that can be restricted to a single genome or across the entire sequence database. Currently Gene3D contains over 3.5 million domain assignments for nearly 5 million proteins including 527 completed genomes. This is available at: http://gene3d.biochem.ucl.ac.uk/

    Metadata

    Item Type: Article
    School: Birkbeck Faculties and Schools > Faculty of Science > School of Computing and Mathematical Sciences
    Research Centres and Institutes: Structural Molecular Biology, Institute of (ISMB), Birkbeck Knowledge Lab
    Depositing User: Administrator
    Date Deposited: 27 Jan 2011 16:07
    Last Modified: 09 Aug 2023 12:30
    URI: https://eprints.bbk.ac.uk/id/eprint/1880

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