{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T22:25:14Z","timestamp":1758925514852,"version":"3.37.3"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2020,8,11]],"date-time":"2020-08-11T00:00:00Z","timestamp":1597104000000},"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\/501100003593","name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","doi-asserted-by":"publisher","award":["457851\/2014-7"],"award-info":[{"award-number":["457851\/2014-7"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","doi-asserted-by":"publisher","award":["051\/2013"],"award-info":[{"award-number":["051\/2013"]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>CONAN is a web application developed to detect specificity determinants and function-related sites by amino acids co-variation networks analysis, emphasizing local coevolutionary constraints. The software allows the characterization of structurally and functionally relevant groups of residues and their relationship with subsets of sequences by automatic cross-referencing with GO terms, UniprotKb annotations and INTERPRO.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CONAN is free and open-source, being distributed in the terms of the GPLV3 license. The software is available as a web application and python script versions and can be accessed at http:\/\/bioinfo.icb.ufmg.br\/conan. We also provide running instructions, the source code and a user guide.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa713","type":"journal-article","created":{"date-parts":[[2020,8,5]],"date-time":"2020-08-05T19:31:54Z","timestamp":1596655914000},"page":"1026-1028","source":"Crossref","is-referenced-by-count":4,"title":["CONAN: a web application to detect specificity determinants and functional sites by amino acids co-variation network analysis"],"prefix":"10.1093","volume":"37","author":[{"given":"N J","family":"Fonseca","sequence":"first","affiliation":[{"name":"Cellular Structure and 3D Bioimaging, European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Genome Campus, Hinxton CB10 1SA, UK"},{"name":"Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais , Belo Horizonte 31270-901, Brazil"}]},{"given":"M Q L","family":"Afonso","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais , Belo Horizonte 31270-901, Brazil"}]},{"given":"L","family":"Carrijo","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais , Belo Horizonte 31270-901, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7121-4952","authenticated-orcid":false,"given":"L","family":"Bleicher","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais , Belo Horizonte 31270-901, Brazil"}]}],"member":"286","published-online":{"date-parts":[[2020,8,11]]},"reference":[{"key":"2023051612173025100_btaa713-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-020-16478-0","article-title":"An evolutionary path to altered cofactor specificity in a metalloenzyme","volume":"11","author":"Barwinska-Sendra","year":"2020","journal-title":"Nat. Commun"},{"key":"2023051612173025100_btaa713-B2","doi-asserted-by":"crossref","first-page":"e27786","DOI":"10.1371\/journal.pone.0027786","article-title":"Using amino acid correlation and community detection algorithms to identify functional determinants in protein families","volume":"6","author":"Bleicher","year":"2011","journal-title":"PLoS One"},{"key":"2023051612173025100_btaa713-B3","doi-asserted-by":"crossref","first-page":"2301","DOI":"10.1109\/TVCG.2011.185","article-title":"D3 data-driven documents","volume":"17","author":"Bostock","year":"2011","journal-title":"IEEE Trans. Visual. Comput. Graph"},{"key":"2023051612173025100_btaa713-B4","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1016\/j.biochi.2015.10.016","article-title":"Coq7p relevant residues for protein activity and stability","volume":"119","author":"Busso","year":"2015","journal-title":"Biochimie"},{"key":"2023051612173025100_btaa713-B5","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1093\/bib\/bbt092","article-title":"A survey on prediction of specificity-determining sites in proteins","volume":"16","author":"Chakraborty","year":"2015","journal-title":"Brief. Bioinform"},{"key":"2023051612173025100_btaa713-B6","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1016\/j.molimm.2019.04.028","article-title":"Structural and immunological characterization of a new nucleotidyltransferase-like antigen from Paracoccidioides brasiliensis","volume":"112","author":"Coitinho","year":"2019","journal-title":"Mol. Immunol"},{"key":"2023051612173025100_btaa713-B7","doi-asserted-by":"crossref","first-page":"1478","DOI":"10.1093\/bioinformatics\/bty846","article-title":"A new method bridging graph theory and residue co-evolutionary networks for specificity determinant positions detection","volume":"35","author":"da Fonseca","year":"2019","journal-title":"Bioinformatics"},{"key":"2023051612173025100_btaa713-B8","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1016\/j.bbrc.2017.01.041","article-title":"Sequence, structure and function relationships in flaviviruses as assessed by evolutive aspects of its conserved non-structural protein domains","volume":"492","author":"da Fonseca","year":"2017","journal-title":"Biochem. Biophys. Res. Commun"},{"key":"2023051612173025100_btaa713-B9","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1007\/s00249-007-0188-5","article-title":"A reduced amino acid alphabet for understanding and designing protein adaptation to mutation","volume":"36","author":"Etchebest","year":"2007","journal-title":"Eur. Biophys. J"},{"key":"2023051612173025100_btaa713-B10","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1016\/j.fgb.2013.06.006","article-title":"Her2p molecular modeling, mutant analysis and intramitochondrial localization","volume":"60","author":"Ferreira-J\u00fanior","year":"2013","journal-title":"Fungal Genet. Biol"},{"key":"2023051612173025100_btaa713-B11","doi-asserted-by":"crossref","first-page":"2096","DOI":"10.1093\/bioinformatics\/btn397","article-title":"BioJava: an open-source framework for bioinformatics","volume":"24","author":"Holland","year":"2008","journal-title":"Bioinformatics"},{"key":"2023051612173025100_btaa713-B12","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1046\/j.1432-1327.1998.2570101.x","article-title":"The laminarinase from thermophilic eubacterium Rhodothermus marinus: conformation, stability, and identification of active site carboxylic residues by site-directed mutagenesis","volume":"257","author":"Krah","year":"1998","journal-title":"Eur. J. Biochem"},{"key":"2023051612173025100_btaa713-B13","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1186\/1471-2164-14-S6-S1","article-title":"Residue correlation networks in nuclear receptors reflect functional specialization and the formation of the nematode-specific P-box","volume":"14 (Suppl. 6","author":"Lima Afonso","year":"2013","journal-title":"BMC Genomics"},{"key":"2023051612173025100_btaa713-B14","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.1021\/acs.jcim.9b00903","article-title":"Coevolved positions represent key functional properties in the trypsin-like serine proteases protein family","volume":"60","author":"Querino Lima Afonso","year":"2020","journal-title":"J. Chem. Inf. Model"},{"key":"2023051612173025100_btaa713-B15","doi-asserted-by":"crossref","first-page":"1322","DOI":"10.1093\/bioinformatics\/btu829","article-title":"3Dmol.js: molecular visualization with WebGL","volume":"31","author":"Rego","year":"2015","journal-title":"Bioinformatics"},{"key":"2023051612173025100_btaa713-B16","doi-asserted-by":"crossref","first-page":"e0177090","DOI":"10.1371\/journal.pone.0177090","article-title":"Structural and functional mapping of Rtg2p determinants involved in retrograde signaling and aging of Saccharomyces cerevisiae","volume":"12","author":"Rios-Anjos","year":"2017","journal-title":"PLoS One"},{"key":"2023051612173025100_btaa713-B17","first-page":"D506","article-title":"UniProt: a worldwide hub of protein knowledge The UniProt Consortium","volume-title":"Nucleic Acids Res","year":"2019"},{"key":"2023051612173025100_btaa713-B18","doi-asserted-by":"crossref","first-page":"e17994","DOI":"10.1371\/journal.pone.0017994","article-title":"Statistically validated networks in bipartite complex systems","volume":"6","author":"Tumminello","year":"2011","journal-title":"PLoS One"},{"key":"2023051612173025100_btaa713-B19","doi-asserted-by":"crossref","first-page":"2040","DOI":"10.1093\/bioinformatics\/btx120","article-title":"ProtVista: visualization of protein sequence annotations","volume":"33","author":"Watkins","year":"2017","journal-title":"Bioinformatics"},{"key":"2023051612173025100_btaa713-B20","doi-asserted-by":"crossref","first-page":"3501","DOI":"10.1093\/bioinformatics\/btw474","article-title":"MSAViewer: interactive JavaScript visualization of multiple sequence alignments","volume":"32","author":"Yachdav","year":"2016","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa713\/34160823\/btaa713.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/7\/1026\/50341189\/btaa713.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/7\/1026\/50341189\/btaa713.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T12:18:46Z","timestamp":1684239526000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/7\/1026\/5891173"}},"subtitle":[],"editor":[{"given":"Pier","family":"Luigi Martelli","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,8,11]]},"references-count":20,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2021,5,17]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa713","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2021,4,1]]},"published":{"date-parts":[[2020,8,11]]}}}