title: Gene3D: expanding the utility of domain assignments.
abstract: Gene3D http://gene3d.biochem.ucl.ac.uk is a database of domain annotations of Ensembl and UniProtKB protein sequences. Domains are predicted using a library of profile HMMs representing 2737 CATH superfamilies. Gene3D has previously featured in the Database issue of NAR and here we report updates to the website and database. The current Gene3D (v14) release has expanded its domain assignments to ∼ 20,000 cellular genomes and over 43 million unique protein sequences, more than doubling the number of protein sequences since our last publication. Amongst other updates, we have improved our Functional Family annotation method. We have also improved the quality and coverage of our 3D homology modelling pipeline of predicted CATH domains. Additionally, the structural models have been expanded to include an extra model organism (Drosophila melanogaster). We also document a number of additional visualization tools in the Gene3D website.
authors.affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK.
authors.forename: Su Datt
authors.initials: SD
authors.lastname: Lam
authors.affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK.
authors.forename: Natalie L
authors.initials: NL
authors.lastname: Dawson
authors.affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK.
authors.forename: Sayoni
authors.initials: S
authors.lastname: Das
authors.affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK.
authors.forename: Ian
authors.initials: I
authors.lastname: Sillitoe
authors.affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Ashford
authors.affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK.
authors.forename: David
authors.initials: D
authors.lastname: Lee
authors.affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK Department of Infectious Disease Epidemiology, Imperial College, St Mary's Campus, Norfolk Place, London W2 1PG, UK.
authors.forename: Sonja
authors.initials: S
authors.lastname: Lehtinen
authors.affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK.
authors.forename: Christine A
authors.initials: CA
authors.lastname: Orengo
authors.affiliation: Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK jonathan.lees@ucl.ac.uk.
authors.forename: Jonathan G
authors.initials: JG
authors.lastname: Lees
mesh_terms: D030562:Databases, Protein; D006801:Humans; D020407:Internet; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D054730:Protein Interaction Domains and Motifs; D017434:Protein Structure, Tertiary / Q000235:genetics