{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:15Z","timestamp":1772138055728,"version":"3.50.1"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2022,9,16]],"date-time":"2022-09-16T00:00:00Z","timestamp":1663286400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100009559","name":"Universidad Nacional de Quilmes","doi-asserted-by":"publisher","award":["PUNQ 1309\/19"],"award-info":[{"award-number":["PUNQ 1309\/19"]}],"id":[{"id":"10.13039\/501100009559","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021778","name":"Agencia Nacional de Promoci\u00f3n de la Investigaci\u00f3n, el Desarrollo Tecnol\u00f3gico y la Innovaci\u00f3n","doi-asserted-by":"publisher","award":["PICT-2018 3457"],"award-info":[{"award-number":["PICT-2018 3457"]}],"id":[{"id":"10.13039\/501100021778","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002923","name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas","doi-asserted-by":"crossref","award":["PIP-2015-2017 11220150100853CO"],"award-info":[{"award-number":["PIP-2015-2017 11220150100853CO"]}],"id":[{"id":"10.13039\/501100002923","id-type":"DOI","asserted-by":"crossref"}]},{"name":"European Union\u2019s Horizon 2020 Research and Innovation Staff Exchange program","award":["778247"],"award-info":[{"award-number":["778247"]}]},{"name":"European Union\u2019s Horizon 2020 Research and Innovation Staff Exchange program","award":["823886"],"award-info":[{"award-number":["823886"]}]},{"DOI":"10.13039\/501100002923","name":"CONICET","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100002923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,10,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>A collection of conformers that exist in a dynamical equilibrium defines the native state of a protein. The structural differences between them describe their conformational diversity, a defining characteristic of the protein with an essential role in multiple cellular processes. Since most proteins carry out their functions by assembling into complexes, we have developed CoDNaS-Q, the first online resource to explore conformational diversity in homooligomeric proteins. It features a curated collection of redundant protein structures with known quaternary structure. CoDNaS-Q integrates relevant annotations that allow researchers to identify and explore the extent and possible reasons of conformational diversity in homooligomeric protein complexes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>CoDNaS-Q is freely accessible at http:\/\/ufq.unq.edu.ar\/codnasq\/ or https:\/\/codnas-q.bioinformatica.org\/home. The data can be retrieved from the website. The source code of the database can be downloaded from https:\/\/github.com\/SfrRonaldo\/codnas-q.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac627","type":"journal-article","created":{"date-parts":[[2022,9,15]],"date-time":"2022-09-15T16:51:07Z","timestamp":1663260667000},"page":"4959-4961","source":"Crossref","is-referenced-by-count":6,"title":["CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0195-3973","authenticated-orcid":false,"given":"Nahuel","family":"Escobedo","sequence":"first","affiliation":[{"name":"Departamento de Ciencia y Tecnolog\u00eda, Universidad Nacional de Quilmes , Buenos Aires B1876BXD, Argentina"},{"name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas , Buenos Aires C1425FQB, Argentina"}]},{"given":"Ronaldo Romario","family":"Tunque Cahui","sequence":"additional","affiliation":[{"name":"Departamento de Ingenier\u00eda, Pontificia Universidad Cat\u00f3lica del Per\u00fa , Lima 15088, Peru"}]},{"given":"Gast\u00f3n","family":"Caruso","sequence":"additional","affiliation":[{"name":"Departamento de Ciencia y Tecnolog\u00eda, Universidad Nacional de Quilmes , Buenos Aires B1876BXD, Argentina"}]},{"given":"Emilio","family":"Garc\u00eda R\u00edos","sequence":"additional","affiliation":[{"name":"Departamento de Ingenier\u00eda, Pontificia Universidad Cat\u00f3lica del Per\u00fa , Lima 15088, Peru"}]},{"given":"Layla","family":"Hirsh","sequence":"additional","affiliation":[{"name":"Departamento de Ingenier\u00eda, Pontificia Universidad Cat\u00f3lica del Per\u00fa , Lima 15088, Peru"}]},{"given":"Alexander Miguel","family":"Monzon","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padova , Padova 35121, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7444-1624","authenticated-orcid":false,"given":"Gustavo","family":"Parisi","sequence":"additional","affiliation":[{"name":"Departamento de Ciencia y Tecnolog\u00eda, Universidad Nacional de Quilmes , Buenos Aires B1876BXD, Argentina"},{"name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas , Buenos Aires C1425FQB, Argentina"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7925-6436","authenticated-orcid":false,"given":"Nicolas","family":"Palopoli","sequence":"additional","affiliation":[{"name":"Departamento de Ciencia y Tecnolog\u00eda, Universidad Nacional de Quilmes , Buenos Aires B1876BXD, Argentina"},{"name":"Consejo Nacional de Investigaciones Cient\u00edficas y T\u00e9cnicas , Buenos Aires C1425FQB, Argentina"}]}],"member":"286","published-online":{"date-parts":[[2022,9,16]]},"reference":[{"key":"2022103112483826500_btac627-B1","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2022103112483826500_btac627-B2","doi-asserted-by":"crossref","first-page":"10480","DOI":"10.1038\/s41598-017-09654-8","article-title":"Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology","volume":"7","author":"Bertoni","year":"2017","journal-title":"Sci. Rep"},{"key":"2022103112483826500_btac627-B3","doi-asserted-by":"crossref","first-page":"1745","DOI":"10.1093\/bioinformatics\/btab858","article-title":"CoDNaS-RNA: a database of conformational diversity in the native state of RNA","volume":"38","author":"Buitr\u00f3n","year":"2021","journal-title":"Bioinformatics"},{"key":"2022103112483826500_btac627-B4","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1146\/annurev-biophys-050511-102222","article-title":"Allostery and the Monod-Wyman-Changeux model after 50 years","volume":"41","author":"Changeux","year":"2012","journal-title":"Annu. Rev. Biophys"},{"key":"2022103112483826500_btac627-B5","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/0079-6107(84)90008-7","article-title":"Protein fluctuations and the thermodynamic uncertainty principle","volume":"44","author":"Cooper","year":"1984","journal-title":"Prog. Biophys. Mol. Biol"},{"key":"2022103112483826500_btac627-B6","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/nmeth.4510","article-title":"PDB-wide identification of biological assemblies from conserved quaternary structure geometry","volume":"15","author":"Dey","year":"2018","journal-title":"Nat. Methods"},{"key":"2022103112483826500_btac627-B7","doi-asserted-by":"crossref","first-page":"1598","DOI":"10.1126\/science.1749933","article-title":"The energy landscapes and motions of proteins","volume":"254","author":"Frauenfelder","year":"1991","journal-title":"Science"},{"key":"2022103112483826500_btac627-B8","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1038\/nature06522","article-title":"Dynamic personalities of proteins","volume":"450","author":"Henzler-Wildman","year":"2007","journal-title":"Nature"},{"key":"2022103112483826500_btac627-B9","doi-asserted-by":"crossref","first-page":"838","DOI":"10.1038\/nature06410","article-title":"Intrinsic motions along an enzymatic reaction trajectory","volume":"450","author":"Henzler-Wildman","year":"2007","journal-title":"Nature"},{"key":"2022103112483826500_btac627-B10","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1016\/S0968-0004(03)00135-X","article-title":"Conformational diversity and protein evolution\u2014a 60-year-old hypothesis revisited","volume":"28","author":"James","year":"2003","journal-title":"Trends Biochem. Sci"},{"key":"2022103112483826500_btac627-B11","doi-asserted-by":"crossref","first-page":"e155","DOI":"10.1371\/journal.pcbi.0020155","article-title":"3D complex: a structural classification of protein complexes","volume":"2","author":"Levy","year":"2006","journal-title":"PLoS Comput. Biol"},{"key":"2022103112483826500_btac627-B12","doi-asserted-by":"crossref","first-page":"e1001870","DOI":"10.1371\/journal.pbio.1001870","article-title":"Protein flexibility facilitates quaternary structure assembly and evolution","volume":"12","author":"Marsh","year":"2014","journal-title":"PLoS Biol"},{"key":"2022103112483826500_btac627-B13","doi-asserted-by":"crossref","first-page":"643","DOI":"10.1016\/j.sbi.2012.08.008","article-title":"Probing the diverse landscape of protein flexibility and binding","volume":"22","author":"Marsh","year":"2012","journal-title":"Curr. Opin. Struct. Biol"},{"key":"2022103112483826500_btac627-B14","doi-asserted-by":"crossref","first-page":"baw038","DOI":"10.1093\/database\/baw038","article-title":"CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state","volume":"2016","author":"Monzon","year":"2016","journal-title":"Database (Oxford)"},{"key":"2022103112483826500_btac627-B15","doi-asserted-by":"crossref","first-page":"e1005398","DOI":"10.1371\/journal.pcbi.1005398","article-title":"Conformational diversity analysis reveals three functional mechanisms in proteins","volume":"13","author":"Monzon","year":"2017","journal-title":"PLoS Comput. Biol"},{"key":"2022103112483826500_btac627-B16","doi-asserted-by":"crossref","first-page":"3486","DOI":"10.1093\/emboj\/cdg359","article-title":"Diversity of protein-protein interactions","volume":"22","author":"Nooren","year":"2003","journal-title":"EMBO J"},{"key":"2022103112483826500_btac627-B17","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1741-7007-10-2","article-title":"Protein dynamics and conformational selection in bidirectional signal transduction","volume":"10","author":"Nussinov","year":"2012","journal-title":"BMC Biol"},{"key":"2022103112483826500_btac627-B18","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1016\/j.str.2012.01.024","article-title":"Detection of spatial correlations in protein structures and molecular complexes","volume":"20","author":"Sippl","year":"2012","journal-title":"Structure"},{"key":"2022103112483826500_btac627-B19","doi-asserted-by":"crossref","first-page":"6516","DOI":"10.1021\/acs.chemrev.5b00562","article-title":"Protein ensembles: how does nature harness thermodynamic fluctuations for life? the diverse functional roles of conformational ensembles in the cell","volume":"116","author":"Wei","year":"2016","journal-title":"Chem. Rev"},{"key":"2022103112483826500_btac627-B20","doi-asserted-by":"crossref","first-page":"D520","DOI":"10.1093\/nar\/gky949","article-title":"Protein data bank: the single global archive for 3D macromolecular structure data","volume":"47","author":"wwPDB consortium","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2022103112483826500_btac627-B21","doi-asserted-by":"crossref","first-page":"3475","DOI":"10.1529\/biophysj.107.114835","article-title":"Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations","volume":"94","author":"Yogurtcu","year":"2008","journal-title":"Biophys. J"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac627\/45958127\/btac627.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/21\/4959\/46697949\/btac627.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/21\/4959\/46697949\/btac627.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,10,31]],"date-time":"2022-10-31T08:50:21Z","timestamp":1667206221000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/21\/4959\/6701961"}},"subtitle":[],"editor":[{"given":"Lenore","family":"Cowen","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,9,16]]},"references-count":21,"journal-issue":{"issue":"21","published-online":{"date-parts":[[2022,9,16]]},"published-print":{"date-parts":[[2022,10,31]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac627","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.02.15.480082","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,11,1]]},"published":{"date-parts":[[2022,9,16]]}}}