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Nucleic Acids Res. 2016 Jan 4;44(D1):D404-9. doi: 10.1093/nar/gkv1231. Epub 2015 Nov 17.

Gene3D: expanding the utility of domain assignments.

Author information

1
Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK.
2
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.
3
Institute of Structural and Molecular Biology, Division of Biosciences, University College London, Gower Street, London, WC1E 6BT, UK jonathan.lees@ucl.ac.uk.

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.

PMID:
26578585
PMCID:
PMC4702871
DOI:
10.1093/nar/gkv1231
[Indexed for MEDLINE]
Free PMC Article

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