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Gene3D: expanding the utility of domain assignments

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...

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Detalles Bibliográficos
Autores principales: Lam, Su Datt, Dawson, Natalie L., Das, Sayoni, Sillitoe, Ian, Ashford, Paul, Lee, David, Lehtinen, Sonja, Orengo, Christine A., Lees, Jonathan G.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702871/
https://www.ncbi.nlm.nih.gov/pubmed/26578585
http://dx.doi.org/10.1093/nar/gkv1231
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author Lam, Su Datt
Dawson, Natalie L.
Das, Sayoni
Sillitoe, Ian
Ashford, Paul
Lee, David
Lehtinen, Sonja
Orengo, Christine A.
Lees, Jonathan G.
author_facet Lam, Su Datt
Dawson, Natalie L.
Das, Sayoni
Sillitoe, Ian
Ashford, Paul
Lee, David
Lehtinen, Sonja
Orengo, Christine A.
Lees, Jonathan G.
author_sort Lam, Su Datt
collection PubMed
description 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.
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spelling pubmed-47028712016-01-07 Gene3D: expanding the utility of domain assignments Lam, Su Datt Dawson, Natalie L. Das, Sayoni Sillitoe, Ian Ashford, Paul Lee, David Lehtinen, Sonja Orengo, Christine A. Lees, Jonathan G. Nucleic Acids Res Database Issue 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. Oxford University Press 2016-01-04 2015-11-17 /pmc/articles/PMC4702871/ /pubmed/26578585 http://dx.doi.org/10.1093/nar/gkv1231 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Lam, Su Datt
Dawson, Natalie L.
Das, Sayoni
Sillitoe, Ian
Ashford, Paul
Lee, David
Lehtinen, Sonja
Orengo, Christine A.
Lees, Jonathan G.
Gene3D: expanding the utility of domain assignments
title Gene3D: expanding the utility of domain assignments
title_full Gene3D: expanding the utility of domain assignments
title_fullStr Gene3D: expanding the utility of domain assignments
title_full_unstemmed Gene3D: expanding the utility of domain assignments
title_short Gene3D: expanding the utility of domain assignments
title_sort gene3d: expanding the utility of domain assignments
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702871/
https://www.ncbi.nlm.nih.gov/pubmed/26578585
http://dx.doi.org/10.1093/nar/gkv1231
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