title: Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis.
abstract: Gene3D (http://gene3d.biochem.ucl.ac.uk) is a database of protein domain structure annotations for protein sequences. Domains are predicted using a library of profile HMMs from 2738 CATH superfamilies. Gene3D assigns domain annotations to Ensembl and UniProt sequence sets including >6000 cellular genomes and >20 million unique protein sequences. This represents an increase of 45% in the number of protein sequences since our last publication. Thanks to improvements in the underlying data and pipeline, we see large increases in the domain coverage of sequences. We have expanded this coverage by integrating Pfam and SUPERFAMILY domain annotations, and we now resolve domain overlaps to provide highly comprehensive composite multi-domain architectures. To make these data more accessible for comparative genome analyses, we have developed novel search algorithms for searching genomes to identify related multi-domain architectures. In addition to providing domain family annotations, we have now developed a pipeline for 3D homology modelling of domains in Gene3D. This has been applied to the human genome and will be rolled out to other major organisms over the next year.
authors.affiliation: Division of Biosciences, Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK, Department of Infectious Disease Epidemiology, Imperial College London, St Mary's Campus, Norfolk Place, London W2 1PG, UK and Robert Koch Institut, Research Group Bioinformatics Ng4, Nordufer 20, 13353 Berlin, Germany.
authors.forename: Jonathan G
authors.initials: JG
authors.lastname: Lees
authors.forename: David
authors.initials: D
authors.lastname: Lee
authors.forename: Romain A
authors.initials: RA
authors.lastname: Studer
authors.forename: Natalie L
authors.initials: NL
authors.lastname: Dawson
authors.forename: Ian
authors.initials: I
authors.lastname: Sillitoe
authors.forename: Sayoni
authors.initials: S
authors.lastname: Das
authors.forename: Corin
authors.initials: C
authors.lastname: Yeats
authors.forename: Benoit H
authors.initials: BH
authors.lastname: Dessailly
authors.forename: Robert
authors.initials: R
authors.lastname: Rentzsch
authors.forename: Christine A
authors.initials: CA
authors.lastname: Orengo
mesh_terms: D030562:Databases, Protein; D016678:Genome; D023281:Genomics; D020407:Internet; D008958:Models, Molecular; D058977:Molecular Sequence Annotation; D017434:Protein Structure, Tertiary / Q000235:genetics; D020539:Sequence Analysis, Protein