{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,26]],"date-time":"2026-06-26T21:52:46Z","timestamp":1782510766709,"version":"3.54.5"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2017,5,2]],"date-time":"2017-05-02T00:00:00Z","timestamp":1493683200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,7,3]]},"DOI":"10.1093\/nar\/gkx346","type":"journal-article","created":{"date-parts":[[2017,4,20]],"date-time":"2017-04-20T23:11:04Z","timestamp":1492729864000},"page":"W24-W29","source":"Crossref","is-referenced-by-count":1537,"title":["BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes"],"prefix":"10.1093","volume":"45","author":[{"given":"Martin Closter","family":"Jespersen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bjoern","family":"Peters","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Morten","family":"Nielsen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paolo","family":"Marcatili","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,5,2]]},"reference":[{"key":"key\n\t\t\t\t20170704095430_B1","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.molimm.2012.06.001","article-title":"Structural analysis of B-cell epitopes in antibody:protein complexes","volume":"53","year":"2013","journal-title":"Mol. Immunol."},{"key":"key\n\t\t\t\t20170704095430_B2","doi-asserted-by":"crossref","first-page":"2002","DOI":"10.1016\/j.bbapap.2014.07.006","article-title":"Antibody informatics for drug discovery","volume":"1844","year":"2014","journal-title":"Biochim. Biophys. Acta"},{"key":"key\n\t\t\t\t20170704095430_B3","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1007\/978-1-4939-6406-2_17","article-title":"In silico prediction of linear B-cell epitopes on proteins","volume":"1484","year":"2017","journal-title":"Methods Mol. Biol."},{"key":"key\n\t\t\t\t20170704095430_B4","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1745-7580-6-S2-S2","article-title":"Recent advances in B-cell epitope prediction methods","volume":"6","year":"2010","journal-title":"Immunome Res."},{"key":"key\n\t\t\t\t20170704095430_B5","doi-asserted-by":"crossref","first-page":"W349","DOI":"10.1093\/nar\/gkv535","article-title":"LYRA, a webserver for lymphocyte receptor structural modeling","volume":"43","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170704095430_B6","doi-asserted-by":"crossref","first-page":"2285","DOI":"10.1093\/bioinformatics\/btt369","article-title":"Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server","volume":"29","year":"2013","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170704095430_B7","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1016\/j.str.2014.02.003","article-title":"Using a combined computational-experimental approach to predict antibody-specific B cell epitopes","volume":"22","year":"2014","journal-title":"Structure"},{"key":"key\n\t\t\t\t20170704095430_B8","doi-asserted-by":"crossref","first-page":"e1000644","DOI":"10.1371\/journal.pcbi.1000644","article-title":"SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models","volume":"6","year":"2010","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20170704095430_B9","doi-asserted-by":"crossref","first-page":"e1002829","DOI":"10.1371\/journal.pcbi.1002829","article-title":"Reliable B cell epitope predictions: impacts of method development and improved benchmarking","volume":"8","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20170704095430_B10","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1745-7580-2-2","article-title":"Improved method for predicting linear B-cell epitopes","volume":"2","year":"2006","journal-title":"Immunome Res."},{"key":"key\n\t\t\t\t20170704095430_B11","first-page":"1","article-title":"Improved method for linear B-cell epitope prediction using antigen's primary sequence","volume":"8","year":"2013","journal-title":"PLoS ONE"},{"key":"key\n\t\t\t\t20170704095430_B12","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1002\/jmr.893","article-title":"Predicting linear B-cell epitopes using string kernels","volume":"21","year":"2008","journal-title":"J. Mol. Recognit."},{"key":"key\n\t\t\t\t20170704095430_B13","first-page":"121","article-title":"Predicting flexible length linear B-cell epitopes","volume":"7","year":"2008","journal-title":"Comput. Syst. Bioinformatics Conf."},{"key":"key\n\t\t\t\t20170704095430_B14","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data bank","volume":"28","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170704095430_B15","doi-asserted-by":"crossref","first-page":"W349","DOI":"10.1093\/nar\/gkv535","article-title":"LYRA, a webserver for lymphocyte receptor structural modeling","volume":"43","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170704095430_B16","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1016\/0022-5193(67)90004-5","article-title":"On the average hydrophobicity of proteins and the relation between it and protein structure","volume":"16","year":"1967","journal-title":"J.Theor. Biol."},{"key":"key\n\t\t\t\t20170704095430_B17","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1016\/0022-2836(83)90041-4","article-title":"Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure","volume":"171","year":"1983","journal-title":"J. Mol. Biol."},{"key":"key\n\t\t\t\t20170704095430_B18","doi-asserted-by":"crossref","first-page":"1664","DOI":"10.1021\/bi00405a042","article-title":"Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution","volume":"27","year":"1988","journal-title":"Biochemistry"},{"key":"key\n\t\t\t\t20170704095430_B19","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/1472-6807-9-51","article-title":"A generic method for assignment of reliability scores applied to solvent accessibility predictions","volume":"9","year":"2009","journal-title":"BMC Struct. Biol."},{"key":"key\n\t\t\t\t20170704095430_B20","doi-asserted-by":"crossref","first-page":"1285","DOI":"10.1126\/science.3287615","article-title":"Measuring the accuracy of diagnostic systems","volume":"240","year":"1988","journal-title":"Science"},{"key":"key\n\t\t\t\t20170704095430_B21","doi-asserted-by":"crossref","first-page":"D405","DOI":"10.1093\/nar\/gku938","article-title":"The immune epitope database (IEDB) 3.0","volume":"43","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20170704095430_B22","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1186\/1471-2105-10-213","article-title":"A comparison of random forest and its Gini importance with standard chemometric methods for the feature selection and classification of spectral data","volume":"10","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"key\n\t\t\t\t20170704095430_B23","doi-asserted-by":"crossref","first-page":"e1002829","DOI":"10.1371\/journal.pcbi.1002829","article-title":"Reliable B cell epitope predictions: impacts of method development and improved benchmarking","volume":"8","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"key\n\t\t\t\t20170704095430_B24","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1093\/protein\/gzt027","article-title":"The indistinguishability of epitopes from protein surface is explained by the distinct binding preferences of each of the six antigen-binding loops","volume":"26","year":"2013","journal-title":"Protein Eng. Des. Sel."},{"key":"key\n\t\t\t\t20170704095430_B25","doi-asserted-by":"crossref","first-page":"2288","DOI":"10.1093\/bioinformatics\/btu190","article-title":"Improving B-cell epitope prediction and its application to global antibody-antigen docking","volume":"30","year":"2014","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20170704095430_B26","doi-asserted-by":"crossref","first-page":"243","DOI":"10.1002\/jmr.893","article-title":"Predicting linear B-cell epitopes using string kernels","volume":"21","year":"2008","journal-title":"J. Mol. Recognit."},{"key":"key\n\t\t\t\t20170704095430_B27","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/1745-7580-6-6","article-title":"Identification of conformational B-cell Epitopes in an antigen from its primary sequence","volume":"6","year":"2010","journal-title":"Immunome Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/45\/W1\/W24\/18137395\/gkx346.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,4,2]],"date-time":"2018-04-02T10:40:59Z","timestamp":1522665659000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article-lookup\/doi\/10.1093\/nar\/gkx346"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,5,2]]},"references-count":27,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2017,5,2]]},"published-print":{"date-parts":[[2017,7,3]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkx346","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,5,2]]}}}