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...

Full description

Saved in:
Bibliographic Details
Published in:Nucleic acids research 2016-01, Vol.44 (D1), p.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: Article
Language:English
Subjects:
Database Issue
Databases, Protein
Humans
Internet
Models, Molecular
Molecular Sequence Annotation
Protein Interaction Domains and Motifs
Protein Structure, Tertiary - genetics
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c447t-c5737b0d27b1dfe0becb27e4c9ac5beb424c891a8976823b7c3676bc578ff2f43
cites cdi_FETCH-LOGICAL-c447t-c5737b0d27b1dfe0becb27e4c9ac5beb424c891a8976823b7c3676bc578ff2f43
container_end_page D409
container_issue D1
container_start_page D404
container_title Nucleic acids research
container_volume 44
creator Lam, Su Datt
Dawson, Natalie L
Das, Sayoni
Sillitoe, Ian
Ashford, Paul
Lee, David
Lehtinen, Sonja
Orengo, Christine A
Lees, Jonathan G
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.
doi_str_mv 10.1093/nar/gkv1231
format article
fullrecord <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_4702871</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1760873402</sourcerecordid><originalsourceid>FETCH-LOGICAL-c447t-c5737b0d27b1dfe0becb27e4c9ac5beb424c891a8976823b7c3676bc578ff2f43</originalsourceid><addsrcrecordid>eNpVkD1PwzAQhi0EoqUwsaOMSCjUX4kdBiRUoCBVYoHZsp1LakicEicV_fcEtVQw3XDPve_pQeic4GuCMzb1up2WH2tCGTlAY8JSGvMspYdojBlOYoK5HKGTEN4xJpwk_BiNaJoImchkjNgcPLD7mwi-VtrnzpdRt4So71zluk3UFFHe1Nr5SIfgSl-D78IpOip0FeBsNyfo7fHhdfYUL17mz7O7RWw5F11sE8GEwTkVhuQFYAPWUAHcZtomBgyn3MqMaJmJVFJmhGWpSM1wJouCFpxN0O02d9WbGnI7dLe6UqvW1brdqEY79X_j3VKVzVpxgakUZAi43AW0zWcPoVO1CxaqSnto-qCISLEUjGM6oFdb1LZNCC0U-xqC1Y9mNWhWO80DffH3sz3765V9A1Gieng</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1760873402</pqid></control><display><type>article</type><title>Gene3D: expanding the utility of domain assignments</title><source>Oxford Journals Open Access Collection</source><source>PubMed Central</source><creator>Lam, Su Datt ; Dawson, Natalie L ; Das, Sayoni ; Sillitoe, Ian ; Ashford, Paul ; Lee, David ; Lehtinen, Sonja ; Orengo, Christine A ; Lees, Jonathan G</creator><creatorcontrib>Lam, Su Datt ; Dawson, Natalie L ; Das, Sayoni ; Sillitoe, Ian ; Ashford, Paul ; Lee, David ; Lehtinen, Sonja ; Orengo, Christine A ; Lees, Jonathan G</creatorcontrib><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.</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkv1231</identifier><identifier>PMID: 26578585</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Database Issue ; Databases, Protein ; Humans ; Internet ; Models, Molecular ; Molecular Sequence Annotation ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary - genetics</subject><ispartof>Nucleic acids research, 2016-01, Vol.44 (D1), p.D404-D409</ispartof><rights>The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><rights>The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. 2016</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c447t-c5737b0d27b1dfe0becb27e4c9ac5beb424c891a8976823b7c3676bc578ff2f43</citedby><cites>FETCH-LOGICAL-c447t-c5737b0d27b1dfe0becb27e4c9ac5beb424c891a8976823b7c3676bc578ff2f43</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702871/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702871/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27922,27923,53789,53791</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26578585$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lam, Su Datt</creatorcontrib><creatorcontrib>Dawson, Natalie L</creatorcontrib><creatorcontrib>Das, Sayoni</creatorcontrib><creatorcontrib>Sillitoe, Ian</creatorcontrib><creatorcontrib>Ashford, Paul</creatorcontrib><creatorcontrib>Lee, David</creatorcontrib><creatorcontrib>Lehtinen, Sonja</creatorcontrib><creatorcontrib>Orengo, Christine A</creatorcontrib><creatorcontrib>Lees, Jonathan G</creatorcontrib><title>Gene3D: expanding the utility of domain assignments</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><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.</description><subject>Database Issue</subject><subject>Databases, Protein</subject><subject>Humans</subject><subject>Internet</subject><subject>Models, Molecular</subject><subject>Molecular Sequence Annotation</subject><subject>Protein Interaction Domains and Motifs</subject><subject>Protein Structure, Tertiary - genetics</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><recordid>eNpVkD1PwzAQhi0EoqUwsaOMSCjUX4kdBiRUoCBVYoHZsp1LakicEicV_fcEtVQw3XDPve_pQeic4GuCMzb1up2WH2tCGTlAY8JSGvMspYdojBlOYoK5HKGTEN4xJpwk_BiNaJoImchkjNgcPLD7mwi-VtrnzpdRt4So71zluk3UFFHe1Nr5SIfgSl-D78IpOip0FeBsNyfo7fHhdfYUL17mz7O7RWw5F11sE8GEwTkVhuQFYAPWUAHcZtomBgyn3MqMaJmJVFJmhGWpSM1wJouCFpxN0O02d9WbGnI7dLe6UqvW1brdqEY79X_j3VKVzVpxgakUZAi43AW0zWcPoVO1CxaqSnto-qCISLEUjGM6oFdb1LZNCC0U-xqC1Y9mNWhWO80DffH3sz3765V9A1Gieng</recordid><startdate>20160104</startdate><enddate>20160104</enddate><creator>Lam, Su Datt</creator><creator>Dawson, Natalie L</creator><creator>Das, Sayoni</creator><creator>Sillitoe, Ian</creator><creator>Ashford, Paul</creator><creator>Lee, David</creator><creator>Lehtinen, Sonja</creator><creator>Orengo, Christine A</creator><creator>Lees, Jonathan G</creator><general>Oxford University Press</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20160104</creationdate><title>Gene3D: expanding the utility of domain assignments</title><author>Lam, Su Datt ; Dawson, Natalie L ; Das, Sayoni ; Sillitoe, Ian ; Ashford, Paul ; Lee, David ; Lehtinen, Sonja ; Orengo, Christine A ; Lees, Jonathan G</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c447t-c5737b0d27b1dfe0becb27e4c9ac5beb424c891a8976823b7c3676bc578ff2f43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Database Issue</topic><topic>Databases, Protein</topic><topic>Humans</topic><topic>Internet</topic><topic>Models, Molecular</topic><topic>Molecular Sequence Annotation</topic><topic>Protein Interaction Domains and Motifs</topic><topic>Protein Structure, Tertiary - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lam, Su Datt</creatorcontrib><creatorcontrib>Dawson, Natalie L</creatorcontrib><creatorcontrib>Das, Sayoni</creatorcontrib><creatorcontrib>Sillitoe, Ian</creatorcontrib><creatorcontrib>Ashford, Paul</creatorcontrib><creatorcontrib>Lee, David</creatorcontrib><creatorcontrib>Lehtinen, Sonja</creatorcontrib><creatorcontrib>Orengo, Christine A</creatorcontrib><creatorcontrib>Lees, Jonathan G</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lam, Su Datt</au><au>Dawson, Natalie L</au><au>Das, Sayoni</au><au>Sillitoe, Ian</au><au>Ashford, Paul</au><au>Lee, David</au><au>Lehtinen, Sonja</au><au>Orengo, Christine A</au><au>Lees, Jonathan G</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Gene3D: expanding the utility of domain assignments</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2016-01-04</date><risdate>2016</risdate><volume>44</volume><issue>D1</issue><spage>D404</spage><epage>D409</epage><pages>D404-D409</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><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.</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>26578585</pmid><doi>10.1093/nar/gkv1231</doi><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 0305-1048
ispartof Nucleic acids research, 2016-01, Vol.44 (D1), p.D404-D409
issn 0305-1048
1362-4962
language eng
recordid cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_4702871
source Oxford Journals Open Access Collection; PubMed Central
subjects Database Issue
Databases, Protein
Humans
Internet
Models, Molecular
Molecular Sequence Annotation
Protein Interaction Domains and Motifs
Protein Structure, Tertiary - genetics
title Gene3D: expanding the utility of domain assignments
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-14T11%3A01%3A13IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Gene3D:%20expanding%20the%20utility%20of%20domain%20assignments&rft.jtitle=Nucleic%20acids%20research&rft.au=Lam,%20Su%20Datt&rft.date=2016-01-04&rft.volume=44&rft.issue=D1&rft.spage=D404&rft.epage=D409&rft.pages=D404-D409&rft.issn=0305-1048&rft.eissn=1362-4962&rft_id=info:doi/10.1093/nar/gkv1231&rft_dat=%3Cproquest_pubme%3E1760873402%3C/proquest_pubme%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c447t-c5737b0d27b1dfe0becb27e4c9ac5beb424c891a8976823b7c3676bc578ff2f43%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=1760873402&rft_id=info:pmid/26578585&rfr_iscdi=true