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1.
Nucleic Acids Res. 2010 Jan;38(Database issue):D296-300. doi: 10.1093/nar/gkp987. Epub 2009 Nov 11.

Gene3D: merging structure and function for a Thousand genomes.

Author information

  • 1Department of Biochemistry and Molecular Biology, University College London, Gower St, London WC1 6BT, UK.

Abstract

Over the last 2 years the Gene3D resource has been significantly improved, and is now more accurate and with a much richer interactive display via the Gene3D website (http://gene3d.biochem.ucl.ac.uk/). Gene3D provides accurate structural domain family assignments for over 1100 genomes and nearly 10,000,000 proteins. A hidden Markov model library, constructed from the manually curated CATH structural domain hierarchy, is used to search UniProt, RefSeq and Ensembl protein sequences. The resulting matches are refined into simple multi-domain architectures using a recently developed in-house algorithm, DomainFinder 3 (available at: ftp://ftp.biochem.ucl.ac.uk/pub/gene3d_data/DomainFinder3/). The domain assignments are integrated with multiple external protein function descriptions (e.g. Gene Ontology and KEGG), structural annotations (e.g. coiled coils, disordered regions and sequence polymorphisms) and family resources (e.g. Pfam and eggNog) and displayed on the Gene3D website. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. Gene3D also provides a set of services, including an interactive genome coverage graph visualizer, DAS annotation resources, sequence search facilities and SOAP services.

PMID:
19906693
[PubMed - indexed for MEDLINE]
PMCID:
PMC2808988
Free PMC Article
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2.
Nucleic Acids Res. 2012 Jan;40(Database issue):D465-71. doi: 10.1093/nar/gkr1181. Epub 2011 Dec 1.

Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis.

Author information

  • 1Institute of Structural and Molecular Biology, University College London, Darwin Building, Gower St, London WC1E 6BT, UK. lees@biochem.ucl.ac.uk

Erratum in

  • Nucleic Acids Res. 2012 May;40(10):4725.

Abstract

Gene3D http://gene3d.biochem.ucl.ac.uk is a comprehensive database of protein domain assignments for sequences from the major sequence databases. Domains are directly mapped from structures in the CATH database or predicted using a library of representative profile HMMs derived from CATH superfamilies. As previously described, Gene3D integrates many other protein family and function databases. These facilitate complex associations of molecular function, structure and evolution. Gene3D now includes a domain functional family (FunFam) level below the homologous superfamily level assignments. Additions have also been made to the interaction data. More significantly, to help with the visualization and interpretation of multi-genome scale data sets, we have developed a new, revamped website. Searching has been simplified with more sophisticated filtering of results, along with new tools based on Cytoscape Web, for visualizing protein-protein interaction networks, differences in domain composition between genomes and the taxonomic distribution of individual superfamilies.

PMID:
22139938
[PubMed - indexed for MEDLINE]
PMCID:
PMC3245158
Free PMC Article
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