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URL: http://gene3d.biochem.ucl.ac.uk/Gene3D/
Proper Citation: Gene3D (RRID:SCR_007672)
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 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.
Abbreviations: Gene3D
Synonyms: Gene3D - Structures assigned to Genomes
Resource Type: software resource, data or information resource, storage service resource, data access protocol, web service, service resource, database, data repository
Defining Citation: PMID:19906693, PMID:18032434
Keywords: protein domain, protein, protein superfamily, hidden markov model, structural domain, genome, sequence, domain assignments, protein structure, bio.tools, FASEB list
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