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Resource:Gene3D

Name: Resource:Gene3D
Description: A large database of CATH protein domain assignments for ENSEMBL genomes and Uniprot sequences. Gene3D is a resource of form studying proteins and the component domains. Gene3D takes the HMM's derived from CATH families and scans them against various sequence databases. By doing this transfer of structural annotation we are able to extend the structural annotation from 1000's of structures to millions of sequences. Strict confidence cut-offs are used to ensure the reliability of the domain assignments. Other external resources are imported into Gene3D to provide complimentary information.

Gene3D imports functional information from sources such as UNIPROT, and KEGG. They also import experimental datasets on request to help researchers integrate there data with the corpus of the literature.

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.

The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG.
Other Name(s): Gene3D - Structures assigned to Genomes
Parent Organization: University College London; London; United Kingdom
Supporting Agency: Wellcome Trust, European Commission, (Framework Program 6), National Institutes of Health, ENFIN
Resource Type(s): Web accessible database, Downloadable database, Web service, Data storage repository
Keywords: protein domain, protein, protein superfamily, hidden Markov model, structural domain, genome, sequence, Domain assignments
Grant: LSHG-CT-2003-503265, LSHG-CT-2004-512092, DE-AC02-065CH11357, LSHG-CT-2005-518254
Abbreviation: Gene3D
Resource: Resource
URL: http://gene3d.biochem.ucl.ac.uk/Gene3D/
PMID: PMID 19906693, 18032434
Id: nif-0000-02877
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Uncurated

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Facts about Resource:Gene3DRDF feed
AbbrevGene3D  +
CurationStatusuncurated  +
DefiningCitationhttp://gene3d.biochem.ucl.ac.uk/Gene3D/  +
DefinitionA large database of CATH protein domain as A large database of CATH protein domain assignments for ENSEMBL genomes and Uniprot sequences. Gene3D is a resource of form studying proteins and the component domains. Gene3D takes CATH domains from Protein Databank (PDB) structures and assigns them to the millions of protein sequences with no PDB structures using Hidden Markov models. Assigning a CATH superfamily to a region of a protein sequence gives information on the gross 3D structure of that region of the protein. CATH superfamilies have a limited set of functions and so the domain assignment provides some functional insights. Furthermore most proteins have several different domains in a specific order, so looking for proteins with a similar domain organization provides further functional insights. Strict confidence cut-offs are used to ensure the reliability of the domain assignments.

Gene3D imports functional information from sources such as UNIPROT, and KEGG. They also import experimental datasets on request to help researchers integrate there data with the corpus of the literature.

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.

The Gene3D web services provide programmatic access to the CATH-Gene3D annotation resources and in-house software tools. These services include Gene3DScan for identifying structural domains within protein sequences, access to pre-calculated annotations for the major sequence databases, and linked functional annotation from UniProt, GO and KEGG.
onal annotation from UniProt, GO and KEGG.
ExampleImageGene3D.PNG  +
GrantCategory:LSHG-CT-2003-503265   +, Category:LSHG-CT-2004-512092   +, Category:DE-AC02-065CH11357   +, and Category:LSHG-CT-2005-518254   +
Has default formThis property is a special property in this wiki.Resource  +
Has roleWeb service  +, Database  +, and Data repository  +
Idnif-0000-02877  +
Is part ofUniversity College London; London; United Kingdom  +
KeywordsProtein domain  +, Protein  +, Protein superfamily  +, Hidden Markov model  +, Structural domain  +, Genome  +, Sequence  +, Domain assignments  +, and Protein structure  +
LabelResource:Gene3D  +
ModifiedDate21 June 2013  +
PMID19906693, 18032434  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +
Supporting AgencyWellcome Trust  +, European Commission  +, (Framework Program 6)  +, ENFIN  +, and National Institutes of Health  +
SynonymGene3D - Structures assigned to Genomes  +