Gene3D: expanding the utility of domain assignments

• Published in: Nucleic acids research Vol. 44; no. D1; pp. D404 - D409
• Main Authors: Lam, Su Datt, Dawson, Natalie L, Das, Sayoni, Sillitoe, Ian, Ashford, Paul, Lee, David, Lehtinen, Sonja, Orengo, Christine A, Lees, Jonathan G
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 04.01.2016
• Subjects: Database Issue; Databases, Protein; Humans; Internet; Models, Molecular; Molecular Sequence Annotation; Protein Interaction Domains and Motifs; Protein Structure, Tertiary - genetics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkv1231

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.