{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T22:58:39Z","timestamp":1785797919137,"version":"3.56.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2022,5,17]],"date-time":"2022-05-17T00:00:00Z","timestamp":1652745600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Research"},{"name":"Universit\u00e9 Paris Cit\u00e9"},{"DOI":"10.13039\/501100000272","name":"National Institute for Health and Medical Research","doi-asserted-by":"crossref","award":["ANR-18-IDEX-0001"],"award-info":[{"award-number":["ANR-18-IDEX-0001"]}],"id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001665","name":"French National Research Agency","doi-asserted-by":"publisher","award":["ANR-21-CE45-0019"],"award-info":[{"award-number":["ANR-21-CE45-0019"]}],"id":[{"id":"10.13039\/501100001665","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Institut du d\u00e9veloppement et des ressources en informatique scientifique, France","award":["A0050710640"],"award-info":[{"award-number":["A0050710640"]}]},{"name":"Institut du d\u00e9veloppement et des ressources en informatique scientifique, France","award":["A0010710172"],"award-info":[{"award-number":["A0010710172"]}]},{"name":"Tr\u00e8s Grand Centre de Calcul","award":["A0090712053"],"award-info":[{"award-number":["A0090712053"]}]},{"name":"Tr\u00e8s Grand Centre de Calcul","award":["A0110712053"],"award-info":[{"award-number":["A0110712053"]}]},{"name":"Grand Equipement National de Calcul Intensif, France"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Understanding the functions and origins of proteins requires splitting these macromolecules into fragments that could be independent in terms of folding, activity, or evolution. For that purpose, structural domains are the typical level of analysis, but shorter segments, such as subdomains and supersecondary structures, are insightful as well. Here, we propose SWORD2, a web server for exploring how an input protein structure may be decomposed into \u2018Protein Units\u2019 that can be hierarchically assembled to delimit structural domains. For each partitioning solution, the relevance of the identified substructures is estimated through different measures. This multilevel analysis is achieved by integrating our previous work on domain delineation, \u2018protein peeling\u2019\u00a0and model quality assessment. We hope that SWORD2 will be useful to biologists searching for key regions in their proteins of interest and to bioinformaticians building datasets of protein structures.\u00a0The web server is freely available online: https:\/\/www.dsimb.inserm.fr\/SWORD2.<\/jats:p>","DOI":"10.1093\/nar\/gkac370","type":"journal-article","created":{"date-parts":[[2022,4,29]],"date-time":"2022-04-29T19:21:30Z","timestamp":1651260090000},"page":"W732-W738","source":"Crossref","is-referenced-by-count":44,"title":["SWORD2: hierarchical analysis of protein 3D structures"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3522-7083","authenticated-orcid":false,"given":"Gabriel","family":"Cretin","sequence":"first","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9 and Universit\u00e9 des Antilles and Universit\u00e9 de la R\u00e9union , INSERM, BIGR, F-75015 Paris, France"},{"name":"Laboratoire d\u2019Excellence GR-Ex , 75015 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3608-5208","authenticated-orcid":false,"given":"Tatiana","family":"Galochkina","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9 and Universit\u00e9 des Antilles and Universit\u00e9 de la R\u00e9union , INSERM, BIGR, F-75015 Paris, France"},{"name":"Laboratoire d\u2019Excellence GR-Ex , 75015 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6680-8104","authenticated-orcid":false,"given":"Yann","family":"Vander\u00a0Meersche","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9 and Universit\u00e9 des Antilles and Universit\u00e9 de la R\u00e9union , INSERM, BIGR, F-75015 Paris, France"},{"name":"Laboratoire d\u2019Excellence GR-Ex , 75015 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7112-5626","authenticated-orcid":false,"given":"Alexandre\u00a0G","family":"de\u00a0Brevern","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9 and Universit\u00e9 des Antilles and Universit\u00e9 de la R\u00e9union , INSERM, BIGR, F-75015 Paris, France"},{"name":"Laboratoire d\u2019Excellence GR-Ex , 75015 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0380-0092","authenticated-orcid":false,"given":"Guillaume","family":"Postic","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris-Saclay, Univ Evry , IBISC, 91020\u00a0Evry-Courcouronnes, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5138-361X","authenticated-orcid":false,"given":"Jean-Christophe","family":"Gelly","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Paris Cit\u00e9 and Universit\u00e9 des Antilles and Universit\u00e9 de la R\u00e9union , INSERM, BIGR, F-75015 Paris, France"},{"name":"Laboratoire d\u2019Excellence GR-Ex , 75015 Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,5,17]]},"reference":[{"key":"2022070423594343500_B1","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1093\/bioinformatics\/bti773","article-title":"Protein peeling\u2019: an approach for splitting a 3D protein structure into compact fragments","volume":"22","author":"Gelly","year":"2006","journal-title":"Bioinformatics"},{"key":"2022070423594343500_B2","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1093\/bioinformatics\/btq610","article-title":"Protein peeling 3D: new tools for analyzing protein structures","volume":"27","author":"Gelly","year":"2011","journal-title":"Bioinformatics"},{"key":"2022070423594343500_B3","doi-asserted-by":"crossref","first-page":"566","DOI":"10.1002\/prot.340230412","article-title":"Knowledge-based protein secondary structure assignment","volume":"23","author":"Frishman","year":"1995","journal-title":"Proteins Struct. Funct. Bioinf."},{"key":"2022070423594343500_B4","doi-asserted-by":"crossref","first-page":"2577","DOI":"10.1002\/bip.360221211","article-title":"Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features","volume":"22","author":"Kabsch","year":"1983","journal-title":"Biopolymers"},{"key":"2022070423594343500_B5","doi-asserted-by":"crossref","first-page":"e1600552","DOI":"10.1126\/sciadv.1600552","article-title":"An ambiguity principle for assigning protein structural domains","volume":"3","author":"Postic","year":"2017","journal-title":"Sci. Adv."},{"key":"2022070423594343500_B6","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1016\/j.csbj.2021.01.041","article-title":"Protein domain identification methods and online resources","volume":"19","author":"Wang","year":"2021","journal-title":"Comput. Struct. Biotechnol. 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