{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T09:27:44Z","timestamp":1740130064290,"version":"3.37.3"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,11,25]],"date-time":"2020-11-25T00:00:00Z","timestamp":1606262400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Marie Sk\u0142odowska-Curie","award":["823886"]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"Abstract<\/jats:title>\n The RepeatsDB database (URL: https:\/\/repeatsdb.org\/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein tandem repeats are ubiquitous in all branches of the tree of life. The accumulation of solved repeat structures provides new possibilities for classification and detection, but also increasing the need for annotation. Here we present RepeatsDB 3.0, which addresses these challenges and presents an extended classification scheme. The major conceptual change compared to the previous version is the hierarchical classification combining top levels based solely on structural similarity (Class &gt; Topology &gt; Fold) with two new levels (Clan &gt; Family) requiring sequence similarity and describing repeat motifs in collaboration with Pfam. Data growth has been addressed with improved mechanisms for browsing the classification hierarchy. A new UniProt-centric view unifies the increasingly frequent annotation of structures from identical or similar sequences. This update of RepeatsDB aligns with our commitment to develop a resource that extracts, organizes and distributes specialized information on tandem repeat protein structures.<\/jats:p>","DOI":"10.1093\/nar\/gkaa1097","type":"journal-article","created":{"date-parts":[[2020,11,20]],"date-time":"2020-11-20T03:54:41Z","timestamp":1605844481000},"page":"D452-D457","source":"Crossref","is-referenced-by-count":41,"title":["RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0011-9397","authenticated-orcid":false,"given":"Lisanna","family":"Paladin","sequence":"first","affiliation":[{"name":"Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58\/B, Padua\u00a035121, Italy"}]},{"given":"Martina","family":"Bevilacqua","sequence":"additional","affiliation":[{"name":"Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58\/B, Padua\u00a035121, Italy"}]},{"given":"Sara","family":"Errigo","sequence":"additional","affiliation":[{"name":"Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58\/B, Padua\u00a035121, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8210-2390","authenticated-orcid":false,"given":"Damiano","family":"Piovesan","sequence":"additional","affiliation":[{"name":"Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58\/B, Padua\u00a035121, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1691-8425","authenticated-orcid":false,"given":"Ivan","family":"Mi\u010deti\u0107","sequence":"additional","affiliation":[{"name":"Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58\/B, Padua\u00a035121, Italy"}]},{"given":"Marco","family":"Necci","sequence":"additional","affiliation":[{"name":"Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58\/B, Padua\u00a035121, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0362-8218","authenticated-orcid":false,"given":"Alexander Miguel","family":"Monzon","sequence":"additional","affiliation":[{"name":"Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58\/B, Padua\u00a035121, Italy"}]},{"given":"Maria Laura","family":"Fabre","sequence":"additional","affiliation":[{"name":"IBBM-CONICET, Dept. of Biological Sciences, La Plata National University, 49 y 115, 1900 La Plata, Argentina"}]},{"given":"Jose\u00a0Luis","family":"Lopez","sequence":"additional","affiliation":[{"name":"IBBM-CONICET, Dept. of Biological Sciences, La Plata National University, 49 y 115, 1900 La Plata, Argentina"}]},{"given":"Juliet F","family":"Nilsson","sequence":"additional","affiliation":[{"name":"IBBM-CONICET, Dept. of Biological Sciences, La Plata National University, 49 y 115, 1900 La Plata, Argentina"}]},{"given":"Javier","family":"Rios","sequence":"additional","affiliation":[{"name":"Dept. of Science and Technology, National University of Quilmes, Roque S\u00e1enz Pe\u00f1a 352, Bernal, Buenos Aires, Argentina"}]},{"given":"Pablo Lorenzano","family":"Menna","sequence":"additional","affiliation":[{"name":"Dept. of Science and Technology, National University of Quilmes, Roque S\u00e1enz Pe\u00f1a 352, Bernal, Buenos Aires, Argentina"}]},{"given":"Maia","family":"Cabrera","sequence":"additional","affiliation":[{"name":"Dept. of Science and Technology, National University of Quilmes, Roque S\u00e1enz Pe\u00f1a 352, Bernal, Buenos Aires, Argentina"}]},{"given":"Martin Gonzalez","family":"Buitron","sequence":"additional","affiliation":[{"name":"Dept. of Science and Technology, National University of Quilmes, Roque S\u00e1enz Pe\u00f1a 352, Bernal, Buenos Aires, Argentina"}]},{"given":"Mariane Gon\u00e7alves","family":"Kulik","sequence":"additional","affiliation":[{"name":"Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, Hans-Dieter-H\u00fcsch-Weg 15, 55128 Mainz, Germany"}]},{"given":"Sebastian","family":"Fernandez-Alberti","sequence":"additional","affiliation":[{"name":"Dept. of Science and Technology, National University of Quilmes, Roque S\u00e1enz Pe\u00f1a 352, Bernal, Buenos Aires, Argentina"}]},{"given":"Maria\u00a0Silvina","family":"Fornasari","sequence":"additional","affiliation":[{"name":"Dept. of Science and Technology, National University of Quilmes, Roque S\u00e1enz Pe\u00f1a 352, Bernal, Buenos Aires, Argentina"}]},{"given":"Gustavo","family":"Parisi","sequence":"additional","affiliation":[{"name":"Dept. of Science and Technology, National University of Quilmes, Roque S\u00e1enz Pe\u00f1a 352, Bernal, Buenos Aires, Argentina"}]},{"given":"Antonio","family":"Lagares","sequence":"additional","affiliation":[{"name":"IBBM-CONICET, Dept. of Biological Sciences, La Plata National University, 49 y 115, 1900 La Plata, Argentina"}]},{"given":"Layla","family":"Hirsh","sequence":"additional","affiliation":[{"name":"Dept. of Engineering, Faculty of Science and Engineering, Pontifical Catholic University of Peru, Av. Universitaria 1801 San Miguel, Lima 32, Lima, Peru"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6650-1711","authenticated-orcid":false,"given":"Miguel\u00a0A","family":"Andrade-Navarro","sequence":"additional","affiliation":[{"name":"Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, Hans-Dieter-H\u00fcsch-Weg 15, 55128 Mainz, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2342-6886","authenticated-orcid":false,"given":"Andrey V","family":"Kajava","sequence":"additional","affiliation":[{"name":"Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237, CNRS, Univ. Montpellier, Montpellier, France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4525-7793","authenticated-orcid":false,"given":"Silvio C E","family":"Tosatto","sequence":"additional","affiliation":[{"name":"Dept. of Biomedical Sciences, University of Padua, Via Ugo Bassi 58\/B, Padua\u00a035121, Italy"}]}],"member":"286","published-online":{"date-parts":[[2020,11,25]]},"reference":[{"key":"2021010313123527000_B1","doi-asserted-by":"crossref","first-page":"D464","DOI":"10.1093\/nar\/gky1004","article-title":"RCSB Protein Data Bank: biological macromolecular structures enabling research and education in fundamental biology, biomedicine, biotechnology and energy","volume":"47","author":"Burley","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021010313123527000_B2","doi-asserted-by":"crossref","first-page":"D280","DOI":"10.1093\/nar\/gky1097","article-title":"CATH: expanding the horizons of structure-based functional annotations for genome sequences","volume":"47","author":"Sillitoe","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2021010313123527000_B3","doi-asserted-by":"crossref","first-page":"D376","DOI":"10.1093\/nar\/gkz1064","article-title":"The SCOP database in 2020: expanded classification of representative family and superfamily domains of known protein structures","volume":"48","author":"Andreeva","year":"2020","journal-title":"Nucleic Acids Res."},{"key":"2021010313123527000_B4","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1016\/S0959-440X(98)80068-7","article-title":"Detection of internal repeats: how common are they","volume":"8","author":"Heringa","year":"1998","journal-title":"Curr. 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