{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T12:13:55Z","timestamp":1771071235429,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2017,9,18]],"date-time":"2017-09-18T00:00:00Z","timestamp":1505692800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/501100007076","name":"Fondazione Italiana per la Ricerca sul Cancro","doi-asserted-by":"publisher","award":["16621"],"award-info":[{"award-number":["16621"]}],"id":[{"id":"10.13039\/501100007076","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005010","name":"Associazione Italiana per la Ricerca sul Cancro","doi-asserted-by":"publisher","award":["IG17753"],"award-info":[{"award-number":["IG17753"]}],"id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The structures contained in the Protein Data Bank (PDB) database are of paramount importance to define our knowledge of folded proteins. While providing mainly circumstantial evidence, PDB data is also increasingly used to define the lack of unique structure, represented by mobile regions and even intrinsic disorder (ID). However, alternative definitions are used by different authors and potentially limit the generality of the analyses being carried out.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here we present Mobi 2.0, a completely re-written version of the Mobi software for the determination of mobile and potentially disordered regions from PDB structures. Mobi 2.0 provides robust definitions of mobility based on four main sources of information: (i) missing residues, (ii) residues with high temperature factors, (iii) mobility between different models of the same structure and (iv) binding to another protein or nucleotide chain. Mobi 2.0 is well suited to aggregate information across different PDB structures for the same UniProt protein sequence, providing consensus annotations. The software is expected to standardize the treatment of mobility, allowing an easier comparison across different studies related to ID.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability<\/jats:title>\n                  <jats:p>Mobi 2.0 provides the structure-based annotation for the MobiDB database. The software is available from URL http:\/\/protein.bio.unipd.it\/mobi2\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx592","type":"journal-article","created":{"date-parts":[[2017,9,15]],"date-time":"2017-09-15T11:08:59Z","timestamp":1505473739000},"page":"122-123","source":"Crossref","is-referenced-by-count":25,"title":["Mobi 2.0: an improved method to define intrinsic disorder, mobility and linear binding regions in protein structures"],"prefix":"10.1093","volume":"34","author":[{"given":"Damiano","family":"Piovesan","sequence":"first","affiliation":[{"name":"Department of Biomedical Sciences, University of Padua Viale G. Colombo 3, Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4525-7793","authenticated-orcid":false,"given":"Silvio C E","family":"Tosatto","sequence":"additional","affiliation":[{"name":"Department of Biomedical Sciences, University of Padua Viale G. Colombo 3, Padova, Italy"},{"name":"CNR Institute of Neuroscience Viale G. Colombo 3, Padova, Italy"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,9,18]]},"reference":[{"key":"2023020208303136800_btx592-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":"2023020208303136800_btx592-B2","doi-asserted-by":"crossref","first-page":"2745","DOI":"10.1093\/bioinformatics\/btp518","article-title":"ANCHOR: web server for predicting protein binding regions in disordered proteins","volume":"25","author":"Doszt\u00e1nyi","year":"2009","journal-title":"Bioinformatics"},{"key":"2023020208303136800_btx592-B3","doi-asserted-by":"crossref","first-page":"3433","DOI":"10.1093\/bioinformatics\/bti541","article-title":"IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content","volume":"21","author":"Doszt\u00e1nyi","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020208303136800_btx592-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":"2023020208303136800_btx592-B5","doi-asserted-by":"crossref","first-page":"1453","DOI":"10.1016\/j.str.2003.10.002","article-title":"Protein disorder prediction: implications for structural proteomics","volume":"11","author":"Linding","year":"2003","journal-title":"Structure"},{"key":"2023020208303136800_btx592-B6","doi-asserted-by":"crossref","first-page":"2916","DOI":"10.1093\/bioinformatics\/btq537","article-title":"MOBI: a web server to define and visualize structural mobility in NMR protein ensembles","volume":"26","author":"Martin","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020208303136800_btx592-B7","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1093\/nar\/gkw315","article-title":"The RING 2.0 web server for high quality residue interaction networks","volume":"44","author":"Piovesan","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023020208303136800_btx592-B8","doi-asserted-by":"crossref","first-page":"D315","DOI":"10.1093\/nar\/gku982","article-title":"MobiDB 2.0: an improved database of intrinsically disordered and mobile proteins","volume":"43","author":"Potenza","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020208303136800_btx592-B9","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1002\/prot.24490","article-title":"The expanded FindCore method for identification of a core atom set for assessment of protein structure prediction","volume":"82","author":"Snyder","year":"2014","journal-title":"Proteins"},{"key":"2023020208303136800_btx592-B10","doi-asserted-by":"crossref","first-page":"D158","DOI":"10.1093\/nar\/gkw1099","article-title":"UniProt: the universal protein knowledgebase","volume":"45","author":"The UniProt Consortium","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023020208303136800_btx592-B11","doi-asserted-by":"crossref","first-page":"D364","DOI":"10.1093\/nar\/gku1028","article-title":"A series of PDB-related databanks for everyday needs","volume":"43","author":"Touw","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023020208303136800_btx592-B12","doi-asserted-by":"crossref","first-page":"D483","DOI":"10.1093\/nar\/gks1258","article-title":"SIFTS: Structure Integration with Function, Taxonomy and Sequences resource","volume":"41","author":"Velankar","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023020208303136800_btx592-B13","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1093\/bioinformatics\/btu625","article-title":"Comprehensive large-scale assessment of intrinsic protein disorder","volume":"31","author":"Walsh","year":"2015","journal-title":"Bioinformatics"},{"key":"2023020208303136800_btx592-B14","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1093\/bib\/bbv082","article-title":"Correct machine learning on protein sequences: a peer-reviewing perspective","volume":"17","author":"Walsh","year":"2016","journal-title":"Brief. 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