{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T07:45:59Z","timestamp":1762674359772,"version":"3.37.3"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2019,11,16]],"date-time":"2019-11-16T00:00:00Z","timestamp":1573862400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000268","name":"Biotechnology and Biological Sciences Research Council","doi-asserted-by":"publisher","award":["BB\/K020013\/1","BB\/M011526\/1","BB\/M011712\/1","BB\/N019172\/1","BB\/N019431\/1"],"award-info":[{"award-number":["BB\/K020013\/1","BB\/M011526\/1","BB\/M011712\/1","BB\/N019172\/1","BB\/N019431\/1"]}],"id":[{"id":"10.13039\/501100000268","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Botnar Foundation","award":["RG91317"],"award-info":[{"award-number":["RG91317"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Genome3D (https:\/\/www.genome3d.eu) is a freely available resource that provides consensus structural annotations for representative protein sequences taken from a selection of model organisms. Since the last NAR update in 2015, the method of data submission has been overhauled, with annotations now being \u2018pushed\u2019 to the database via an API. As a result, contributing groups are now able to manage their own structural annotations, making the resource more flexible and maintainable. The new submission protocol brings a number of additional benefits including: providing instant validation of data and avoiding the requirement to synchronise releases between resources. It also makes it possible to implement the submission of these structural annotations as an automated part of existing internal workflows. In turn, these improvements facilitate Genome3D being opened up to new prediction algorithms and groups. For the latest release of Genome3D (v2.1), the underlying dataset of sequences used as prediction targets has been updated using the latest reference proteomes available in UniProtKB. A number of new reference proteomes have also been added of particular interest to the wider scientific community: cow, pig, wheat and mycobacterium tuberculosis. These additions, along with improvements to the underlying predictions from contributing resources, has ensured that the number of annotations in Genome3D has nearly doubled since the last NAR update article. The new API has also been used to facilitate the dissemination of Genome3D data into InterPro, thereby widening the visibility of both the annotation data and annotation algorithms.<\/jats:p>","DOI":"10.1093\/nar\/gkz967","type":"journal-article","created":{"date-parts":[[2019,11,7]],"date-time":"2019-11-07T20:10:52Z","timestamp":1573157452000},"page":"D314-D319","source":"Crossref","is-referenced-by-count":14,"title":["Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation"],"prefix":"10.1093","volume":"48","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1091-9144","authenticated-orcid":false,"given":"Ian","family":"Sillitoe","sequence":"first","affiliation":[{"name":"Institute of Structural and Molecular Biology, UCL, Gower Street, London WC1E 6BT, UK"}]},{"given":"Antonina","family":"Andreeva","sequence":"first","affiliation":[{"name":"MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK"}]},{"given":"Tom L","family":"Blundell","sequence":"first","affiliation":[{"name":"Department of Biochemistry, University of Cambridge, Old Addenbrooke\u2019s Site, 80 Tennis Court Road, Cambridge CB2 0QH, UK"}]},{"given":"Daniel W A","family":"Buchan","sequence":"first","affiliation":[{"name":"Department of Computer Science, UCL, Gower Street, London WC1E 6BT, UK"},{"name":"The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8626-2148","authenticated-orcid":false,"given":"Robert D","family":"Finn","sequence":"first","affiliation":[{"name":"European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK"}]},{"given":"Julian","family":"Gough","sequence":"first","affiliation":[{"name":"MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK"}]},{"given":"David","family":"Jones","sequence":"first","affiliation":[{"name":"Department of Computer Science, UCL, Gower Street, London WC1E 6BT, UK"},{"name":"The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK"}]},{"given":"Lawrence A","family":"Kelley","sequence":"first","affiliation":[{"name":"Centre for Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK"}]},{"given":"Typhaine","family":"Paysan-Lafosse","sequence":"first","affiliation":[{"name":"European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK"}]},{"given":"Su Datt","family":"Lam","sequence":"first","affiliation":[{"name":"Institute of Structural and Molecular Biology, UCL, Gower Street, London WC1E 6BT, UK"},{"name":"Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor 43600, Malaysia"}]},{"given":"Alexey G","family":"Murzin","sequence":"first","affiliation":[{"name":"MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK"}]},{"given":"Arun Prasad","family":"Pandurangan","sequence":"first","affiliation":[{"name":"MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK"}]},{"given":"Gustavo A","family":"Salazar","sequence":"first","affiliation":[{"name":"European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK"}]},{"given":"Marcin J","family":"Skwark","sequence":"first","affiliation":[{"name":"Department of Biochemistry, University of Cambridge, Old Addenbrooke\u2019s Site, 80 Tennis Court Road, Cambridge CB2 0QH, UK"}]},{"given":"Michael J E","family":"Sternberg","sequence":"first","affiliation":[{"name":"Centre for Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK"}]},{"given":"Sameer","family":"Velankar","sequence":"first","affiliation":[{"name":"European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK"}]},{"given":"Christine","family":"Orengo","sequence":"first","affiliation":[{"name":"Institute of Structural and Molecular Biology, UCL, Gower Street, London WC1E 6BT, UK"}]}],"member":"286","published-online":{"date-parts":[[2019,11,16]]},"reference":[{"key":"2020040805351993100_B1","doi-asserted-by":"crossref","first-page":"D301","DOI":"10.1093\/nar\/gkl971","article-title":"The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data","volume":"35","author":"Berman","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2020040805351993100_B2","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","author":"The","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020040805351993100_B3","doi-asserted-by":"crossref","first-page":"D754","DOI":"10.1093\/nar\/gkx1098","article-title":"Ensembl 2018","volume":"46","author":"Zerbino","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020040805351993100_B4","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1016\/S0022-2836(05)80134-2","article-title":"SCOP: A structural classification of proteins database for the investigation of sequences and structures","volume":"47","author":"Murzin","year":"1995","journal-title":"J. Mol. Biol."},{"key":"2020040805351993100_B5","doi-asserted-by":"crossref","first-page":"D289","DOI":"10.1093\/nar\/gkw1098","article-title":"CATH: An expanded resource to predict protein function through structure and sequence","volume":"45","author":"Dawson","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"2020040805351993100_B6","doi-asserted-by":"crossref","first-page":"D499","DOI":"10.1093\/nar\/gks1266","article-title":"Genome3D: aUK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains","volume":"41","author":"Lewis","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2020040805351993100_B7","doi-asserted-by":"crossref","first-page":"D382","DOI":"10.1093\/nar\/gku973","article-title":"Genome3D: exploiting structure to help users understand their sequences","volume":"43","author":"Lewis","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2020040805351993100_B8","doi-asserted-by":"crossref","first-page":"W563","DOI":"10.1093\/nar\/gkq427","article-title":"Protein annotation and modelling servers at University College London","volume":"38","author":"Buchan","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"2020040805351993100_B9","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1006\/jmbi.2001.4762","article-title":"FUGUE: Sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties","volume":"310","author":"Shi","year":"2001","journal-title":"J. Mol. Biol."},{"key":"2020040805351993100_B10","doi-asserted-by":"crossref","first-page":"D1282","DOI":"10.1093\/nar\/gkx1187","article-title":"Gene3D: Extensive prediction of globular domains in proteins","volume":"46","author":"Lewis","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2020040805351993100_B11","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modeling, prediction and analysis","volume":"10","author":"Kelley","year":"2015","journal-title":"Nat. Protoc."},{"key":"2020040805351993100_B12","doi-asserted-by":"crossref","first-page":"D490","DOI":"10.1093\/nar\/gky1130","article-title":"The SUPERFAMILY 2.0 database: a significant proteome update and a new webserver","volume":"47","author":"Pandurangan","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020040805351993100_B13","doi-asserted-by":"crossref","first-page":"D351","DOI":"10.1093\/nar\/gky1100","article-title":"InterPro in 2019: improving coverage, classification and access to protein sequence annotations","volume":"47","author":"Mitchell","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2020040805351993100_B14","doi-asserted-by":"crossref","first-page":"2040","DOI":"10.1093\/bioinformatics\/btx120","article-title":"ProtVista: visualization of protein sequence annotations","volume":"33","author":"Watkins","year":"2017","journal-title":"Bioinformatics"},{"key":"2020040805351993100_B15","doi-asserted-by":"crossref","first-page":"D486","DOI":"10.1093\/nar\/gkx1070","article-title":"PDBe: towards reusable data delivery infrastructure at protein data bank in Europe","volume":"46","author":"Mir","year":"2018","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/D1\/D314\/33024566\/gkz967.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/48\/D1\/D314\/33024566\/gkz967.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,4,8]],"date-time":"2020-04-08T09:35:34Z","timestamp":1586338534000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/48\/D1\/D314\/5626529"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,11,16]]},"references-count":15,"journal-issue":{"issue":"D1","published-online":{"date-parts":[[2019,11,16]]},"published-print":{"date-parts":[[2020,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkz967","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"type":"print","value":"0305-1048"},{"type":"electronic","value":"1362-4962"}],"subject":[],"published-other":{"date-parts":[[2020,1,8]]},"published":{"date-parts":[[2019,11,16]]}}}