{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,10]],"date-time":"2026-01-10T21:34:02Z","timestamp":1768080842708,"version":"3.49.0"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2019,7,2]],"date-time":"2019-07-02T00:00:00Z","timestamp":1562025600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Education, Youth and Sports of the Czech Republic"},{"name":"CEITEC 2020","award":["LQ1601"],"award-info":[{"award-number":["LQ1601"]}]},{"name":"European Union\u2019s Horizon 2020","award":["676559"],"award-info":[{"award-number":["676559"]}]},{"name":"European Union\u2019s Horizon 2020","award":["LM2015047"],"award-info":[{"award-number":["LM2015047"]}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["CZ.02.1.01\/0.0\/0.0\/16_013\/0001777"],"award-info":[{"award-number":["CZ.02.1.01\/0.0\/0.0\/16_013\/0001777"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"European Regional Development Fund","doi-asserted-by":"publisher","award":["ATCZ40"],"award-info":[{"award-number":["ATCZ40"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Grant Agency of Masaryk University","award":["MUNI\/A\/1503\/2018"],"award-info":[{"award-number":["MUNI\/A\/1503\/2018"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Structures in PDB tend to contain errors. This is a very serious issue for authors that rely on such potentially problematic data. The community of structural biologists develops validation methods as countermeasures, which are also included in the PDB deposition system. But how are these validation efforts influencing the structure quality of subsequently published data? Which quality aspects are improving, and which remain problematic? We developed ValTrendsDB, a database that provides the results of an extensive exploratory analysis of relationships between quality criteria, size and metadata of biomacromolecules. Key input data are sourced from PDB. The discovered trends are presented via precomputed information-rich plots. ValTrendsDB also supports the visualization of a set of user-defined structures on top of general quality trends. Therefore, ValTrendsDB enables users to see the quality of structures published by selected author, laboratory or journal, discover quality outliers, etc. ValTrendsDB is updated weekly.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Freely accessible at http:\/\/ncbr.muni.cz\/ValTrendsDB. The web interface was implemented in JavaScript. The database was implemented in C++.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz532","type":"journal-article","created":{"date-parts":[[2019,6,29]],"date-time":"2019-06-29T03:10:49Z","timestamp":1561777849000},"page":"5389-5390","source":"Crossref","is-referenced-by-count":3,"title":["ValTrendsDB: bringing Protein Data Bank validation information closer to the user"],"prefix":"10.1093","volume":"35","author":[{"given":"Vladim\u00edr","family":"Horsk\u00fd","sequence":"first","affiliation":[{"name":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University , Brno, Czech Republic"},{"name":"CEITEC \u2013 Central European Institute of Technology , Masaryk University, Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Veronika","family":"Bendov\u00e1","sequence":"additional","affiliation":[{"name":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University , Brno, Czech Republic"},{"name":"CEITEC \u2013 Central European Institute of Technology , Masaryk University, Brno, Czech Republic"},{"name":"Institute of Mathematics and Statistics , Faculty of Science, Masaryk University, Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dominik","family":"Tou\u0161ek","sequence":"additional","affiliation":[{"name":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University , Brno, Czech Republic"},{"name":"CEITEC \u2013 Central European Institute of Technology , Masaryk University, Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jaroslav","family":"Ko\u010da","sequence":"additional","affiliation":[{"name":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University , Brno, Czech Republic"},{"name":"CEITEC \u2013 Central European Institute of Technology , Masaryk University, Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Radka","family":"Svobodov\u00e1","sequence":"additional","affiliation":[{"name":"National Centre for Biomolecular Research, Faculty of Science, Masaryk University , Brno, Czech Republic"},{"name":"CEITEC \u2013 Central European Institute of Technology , Masaryk University, Brno, Czech Republic"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,7,2]]},"reference":[{"key":"2023013108413486900_btz532-B1","doi-asserted-by":"crossref","first-page":"2133","DOI":"10.1021\/ci049780b","article-title":"Retrieval of crystallographically-derived molecular geometry information","volume":"44","author":"Bruno","year":"2004","journal-title":"J. Chem. Inf. Comput. Sci"},{"key":"2023013108413486900_btz532-B2","first-page":"D520","article-title":"Protein Data Bank: the single global archive for 3D macromolecular structure data","volume":"47","author":"Burley","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023013108413486900_btz532-B3","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1107\/S0907444909042073","article-title":"MolProbity: all-atom structure validation for macromolecular crystallography","volume":"66","author":"Chen","year":"2010","journal-title":"Acta Crystallogr. D Biol. Crystallogr"},{"key":"2023013108413486900_btz532-B4","doi-asserted-by":"crossref","first-page":"1916","DOI":"10.1016\/j.str.2017.10.009","article-title":"Validation of structures in the Protein Data Bank","volume":"25","author":"Gore","year":"2017","journal-title":"Structure"},{"key":"2023013108413486900_btz532-B5","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1107\/S1744309112008421","article-title":"Detection and analysis of unusual features in the structural model and structure-factor data of a birch pollen allergen","volume":"68","author":"Rupp","year":"2012","journal-title":"Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun"},{"key":"2023013108413486900_btz532-B6","doi-asserted-by":"crossref","first-page":"D369","DOI":"10.1093\/nar\/gku1118","article-title":"ValidatorDB: database of up-to-date validation results for ligands and non-standard residues from the Protein Data Bank","volume":"43","author":"Sehnal","year":"2015","journal-title":"Nucleic Acids Res. Database Issue"},{"key":"2023013108413486900_btz532-B7","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1093\/bioinformatics\/btu789","article-title":"The chemical component dictionary: complete descriptions of constituent molecules in experimentally determined 3D macromolecules in the Protein Data Bank","volume":"31","author":"Westbrook","year":"2015","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz532\/28968670\/btz532.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/24\/5389\/48978590\/bioinformatics_35_24_5389.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/24\/5389\/48978590\/bioinformatics_35_24_5389.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T18:11:37Z","timestamp":1675188697000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/24\/5389\/5526874"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2019,7,2]]},"references-count":7,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2019,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz532","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,12,15]]},"published":{"date-parts":[[2019,7,2]]}}}