title: Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database.
abstract: We present a novel web-based resource, Gene3D, of precalculated structural assignments to gene sequences and whole genomes. This resource assigns structural domains from the CATH database to whole genes and links these to their curated functional and structural annotations within the CATH domain structure database, the functional Dictionary of Homologous Superfamilies (DHS) and PDBsum. Currently Gene3D provides annotation for 36 complete genomes (two eukaryotes, six archaea, and 28 bacteria). On average, between 30% and 40% of the genes of a given genome can be structurally annotated. Matches to structural domains are found using the profile-based method (PSI-BLAST). and a novel protocol, DRange, is used to resolve conflicts in matches involving different homologous superfamilies.
authors.affiliation: Biomolecular Structure and Modelling Group, Department of Biochemistry and Molecular Biology, University College London, London, WC1E 6BT, United Kingdom.
authors.forename: Daniel W A
authors.initials: DW
authors.lastname: Buchan
authors.forename: Adrian J
authors.initials: AJ
authors.lastname: Shepherd
authors.forename: David
authors.initials: D
authors.lastname: Lee
authors.forename: Frances M G
authors.initials: FM
authors.lastname: Pearl
authors.forename: Stuart C G
authors.initials: SC
authors.lastname: Rison
authors.forename: Janet M
authors.initials: JM
authors.lastname: Thornton
authors.forename: Christine A
authors.initials: CA
authors.lastname: Orengo
mesh_terms: D000818:Animals; D019843:Archaeal Proteins / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D030541:Databases, Genetic / Q000706:statistics & numerical data; D030562:Databases, Protein; D005796:Genes / Q000235:genetics*; D019766:Genes, Archaeal / Q000235:genetics; D005798:Genes, Bacterial / Q000235:genetics; D016678:Genome; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D020407:Internet; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D012984:Software / Q000706:statistics & numerical data
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D011506:Proteins