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Liu","year":"2010","journal-title":"Journal of proteome research"},{"issue":"7","key":"ref67","doi-asserted-by":"crossref","first-page":"1431","DOI":"10.1021\/ac981012u","article-title":"18O-labeling of N-glycosylation sites to improve the identification of gel-separated glycoproteins using peptide mass mapping and database searching","volume":"71","author":"B Kuster","year":"1999","journal-title":"Analytical chemistry"},{"issue":"3","key":"ref68","doi-asserted-by":"crossref","first-page":"e1004767","DOI":"10.1371\/journal.ppat.1004767","article-title":"Comprehensive antigenic map of a cleaved soluble HIV-1 envelope trimer","volume":"11","author":"R Derking","year":"2015","journal-title":"PLoS pathogens"},{"issue":"3","key":"ref69","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1007\/BF00994018","article-title":"Support-vector networks","volume":"20","author":"C Cortes","year":"1995","journal-title":"Machine 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of HIV envelope glycoprotein","volume":"8","author":"L Cao","year":"2017","journal-title":"Nature communications"},{"issue":"2","key":"ref74","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1016\/j.cell.2008.11.047","article-title":"Cotranslational and posttranslational N-glycosylation of polypeptides by distinct mammalian OST isoforms","volume":"136","author":"C Ruiz-Canada","year":"2009","journal-title":"Cell"},{"issue":"2","key":"ref75","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1093\/glycob\/cwh008","article-title":"Statistical analysis of the protein environment of N-glycosylation sites: implications for occupancy, structure, and folding","volume":"14","author":"AJ Petrescu","year":"2004","journal-title":"Glycobiology"},{"issue":"17","key":"ref76","doi-asserted-by":"crossref","first-page":"9538","DOI":"10.1128\/JVI.01739-14","article-title":"Characterization and immunogenicity of a novel mosaic M HIV-1 gp140 trimer","volume":"88","author":"JP Nkolola","year":"2014","journal-title":"Journal of virology"},{"issue":"10","key":"ref77","doi-asserted-by":"crossref","first-page":"e1005094","DOI":"10.1371\/journal.pcbi.1005094","article-title":"Effect of Glycosylation on an Immunodominant Region in the V1V2 Variable Domain of the HIV-1 Envelope gp120 Protein","volume":"12","author":"J Tian","year":"2016","journal-title":"PLoS computational biology"},{"issue":"6215","key":"ref78","doi-asserted-by":"crossref","first-page":"1380","DOI":"10.1126\/science.1259206","article-title":"HIV antibodies. Antigen modification regulates competition of broad and narrow neutralizing HIV antibodies","volume":"346","author":"AT McGuire","year":"2014","journal-title":"Science"},{"issue":"Pt 10","key":"ref79","doi-asserted-by":"crossref","first-page":"2099","DOI":"10.1107\/S1399004715013917","article-title":"Complete epitopes for vaccine design derived from a crystal structure of the broadly neutralizing antibodies PGT128 and 8ANC195 in complex with an HIV-1 Env trimer","volume":"71","author":"L Kong","year":"2015","journal-title":"Acta crystallographica Section D, Biological crystallography"},{"issue":"5","key":"ref80","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1093\/bioinformatics\/17.5.415","article-title":"Retrieval and on-the-fly alignment of sequence fragments from the HIV database","volume":"17","author":"B Gaschen","year":"2001","journal-title":"Bioinformatics"},{"issue":"5","key":"ref81","doi-asserted-by":"crossref","first-page":"674","DOI":"10.1002\/rcm.2874","article-title":"A potential pitfall in 18O-based N-linked glycosylation site mapping","volume":"21","author":"PM Angel","year":"2007","journal-title":"Rapid Commun Mass Spectrom"},{"issue":"3","key":"ref82","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/1961189.1961199","article-title":"LIBSVM: A library for support vector machines","volume":"2","author":"C-C Chang","year":"2011","journal-title":"ACM Trans Intell Syst Technol"},{"key":"ref83","unstructured":"Ng A. Machine Learning: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.coursera.org\/learn\/machine-learning\/\" xlink:type=\"simple\">https:\/\/www.coursera.org\/learn\/machine-learning\/<\/ext-link>; 2016. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.coursera.org\/learn\/machine-learning\/\" xlink:type=\"simple\">https:\/\/www.coursera.org\/learn\/machine-learning\/<\/ext-link>."}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006093","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,5,2]],"date-time":"2018-05-02T00:00:00Z","timestamp":1525219200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006093","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,19]],"date-time":"2018-10-19T15:41:30Z","timestamp":1539963690000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006093"}},"subtitle":[],"editor":[{"given":"Greg","family":"Tucker-Kellogg","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,4,20]]},"references-count":83,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2018,4,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006093","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1006093","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,4,20]]}}}