D296–D300 Nucleic Acids Research, 2010, Vol. 38, Database issue doi:10.1093/nar/gkp987 Published online 11 November 2009 Gene3D: merging structure and function for a Thousand genomes Jonathan Lees, Corin Yeats*, Oliver Redfern, Andrew Clegg and Christine Orengo Department of Biochemistry and Molecular Biology, University College London, Gower St. London, WC1 6BT, UK Received September 15, 2009; Revised October 15, 2009; Accepted October 16, 2009 ABSTRACT Over the last 2 years the Gene3D resource has been significantly improved, and is now more accurate and with a much richer interactive display via the Gene3D website (http://gene3d.biochem.ucl.ac .uk/). Gene3D provides accurate structural domain family assignments for over 1100 genomes and nearly 10 000 000 proteins. A hidden Markov model library, constructed from the manually curated CATH structural domain hierarchy, is used to search UniProt, RefSeq and Ensembl protein sequences. The resulting matches are refined into simple multi-domain architectures using a recently developed in-house algorithm, DomainFinder 3 (available at: ftp://ftp.biochem.ucl.ac.uk/ pub/gene3d_data/DomainFinder3/). The domain assignments are integrated with multiple external protein function descriptions (e.g. Gene Ontology and KEGG), structural annotations (e.g. coiled coils, disordered regions and sequence polymorphisms) and family resources (e.g. Pfam and eggNog) and displayed on the Gene3D website. 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. Gene3D also provides a set of services, including an interactive genome coverage graph visualizer, DAS annotation resources, sequence search facilities and SOAP services. INTRODUCTION Gene3D uses the manually curated protein domain assignments from CATH (1) to generate accurate protein domain architecture predictions for over 1000 genomes, as well as the UniProt (2) and RefSeq (3) protein sequence databases. These assignments can be queried, and the results visualized via the Gene3D website. Also displayed are other structural features, such as active sites and disordered regions from Disopred2 (4), and functional terms from UniProt, InterPro (5), the Gene Ontology (6), KEGG (7) and others (Table 1). The website enables complex sub- querying with these terms, giving the user the ability to retrieve information both for global studies and detailed analyses of function by molecular biologists. Gene3D also provides multiple web services, including DAS feature annotation sources and a set of SOAP XML services. The CATH domain database provides a compendium of domains found in the protein structures deposited in the wwPDB (8), grouping them into a hierarchy based on homology relationships and structural features. Domain boundaries and superfamily assignments are determined using manual curation and automated evidence-gathering tools. For each superfamily (the CATH ‘H(omology)- level’) one or more representatives are selected and a set of sequence proﬁles generated. From these hidden Markov model (Hmmer)3 (http://hmmer.janelia.org/) models are built and, in combination with a recently developed in-house method for resolving conﬂicting matches (DomainFinder 3), accurate domain architectures are assigned. DomainFinder 3 is a novel algorithm that uses heaviest-weighted clique ﬁnding to optimize the selec- tion of matches into a multi-domain architecture, and has signiﬁcantly improved the overall quality of the assignments (paper submitted). Over the last 2 years, the underlying technology and software powering the Gene3D resource have been re-implemented, allowing faster generation of releases, easier updates of imported annotations and quicker, more sophisticated querying. These and other improvements are described in the following sections. IMPROVED DOMAIN ASSIGNMENT ACCURACY A total of 10 013 non-redundant domain representatives were selected for all 2386 superfamilies in CATH v.3.3.0, *To whom correspondence should be addressed. Tel: +207 679 3890; Fax: +207 679 7193; Email: yeats@biochem.ucl.ac.uk The authors wish it to be known that, in their opinion, the ﬁrst two authors should be regarded as joint First Authors. The Author(s) 2009. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.