{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T10:32:53Z","timestamp":1790937173431,"version":"4.1.0"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"12","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Accurate prediction of B-cell epitopes is an important goal of computational immunology. Up to 90% of B-cell epitopes are discontinuous in nature, yet most predictors focus on linear epitopes. Even when the tertiary structure of the antigen is available, the accurate prediction of B-cell epitopes remains challenging.<\/jats:p>\n               <jats:p>Results: Our predictor, PEPITO, uses a combination of amino-acid propensity scores and half sphere exposure values at multiple distances to achieve state-of-the-art performance. PEPITO achieves an area under the curve (AUC) of 75.4 on the Discotope dataset. Additionally, we benchmark PEPITO as well as the Discotope predictor on the more recent Epitome dataset, achieving AUCs of 68.3 and 66.0, respectively.<\/jats:p>\n               <jats:p>Availability: PEPITO is available as part of the SCRATCH suite of protein structure predictors via www.igb.uci.edu.<\/jats:p>\n               <jats:p>Contact: \u00a0pfbaldi@ics.uci.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn199","type":"journal-article","created":{"date-parts":[[2008,4,29]],"date-time":"2008-04-29T00:43:51Z","timestamp":1209429831000},"page":"1459-1460","source":"Crossref","is-referenced-by-count":237,"title":["PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure"],"prefix":"10.1093","volume":"24","author":[{"given":"Michael J.","family":"Sweredoski","sequence":"first","affiliation":[{"name":"1 Department of Computer Science and 2Institute for Genomics and Bioinformatics, University of California, Irvine, 92697-3435, California, USA"},{"name":"1 Department of Computer Science and 2Institute for Genomics and Bioinformatics, University of California, Irvine, 92697-3435, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pierre","family":"Baldi","sequence":"additional","affiliation":[{"name":"1 Department of Computer Science and 2Institute for Genomics and Bioinformatics, University of California, Irvine, 92697-3435, California, USA"},{"name":"1 Department of Computer Science and 2Institute for Genomics and Bioinformatics, University of California, Irvine, 92697-3435, California, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2008,4,28]]},"reference":[{"key":"2023020210100916800_B1","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1016\/S0264-410X(99)00329-1","article-title":"Predictive estimation of protein linear epitopes by using the program PEOPLE","volume":"18","author":"Alix","year":"1999","journal-title":"Vaccine"},{"key":"2023020210100916800_B2","doi-asserted-by":"crossref","first-page":"2558","DOI":"10.1110\/ps.062405906","article-title":"Prediction of residues in discontinuous B-cell epitopes using protein 3D structures","volume":"15","author":"Andersen","year":"2006","journal-title":"Protein Sci"},{"key":"2023020210100916800_B3","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1110\/ps.041059505","article-title":"Benchmarking B cell epitope prediction: underperformance of existing methods","volume":"14","author":"Blythe","year":"2005","journal-title":"Protein Sci"},{"key":"2023020210100916800_B4","doi-asserted-by":"crossref","first-page":"w72","DOI":"10.1093\/nar\/gki396","article-title":"SCRATCH: a protein structure and structural feature prediction server","volume":"33","author":"Cheng","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023020210100916800_B5","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1002\/jmr.815","article-title":"Toward a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools","volume":"20","author":"Greenbaum","year":"2007","journal-title":"J. Mol. Recognit"},{"key":"2023020210100916800_B6","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1002\/prot.20379","article-title":"An amino acids has two sides: a new 2D measure provides a different view of solvent exposure","volume":"59","author":"Hamelryck","year":"2005","journal-title":"Prot. Struct. Func. Bioinform"},{"key":"2023020210100916800_B7","doi-asserted-by":"crossref","first-page":"3824","DOI":"10.1073\/pnas.78.6.3824","article-title":"Prediction of protein antigenic determinants from amino acid sequences","volume":"78","author":"Hopp","year":"1981","journal-title":"Proc. Natl Acad. Sci"},{"key":"2023020210100916800_B8","doi-asserted-by":"crossref","first-page":"w168","DOI":"10.1093\/nar\/gki460","article-title":"CEP: a conformational epitope prediction server","volume":"33","author":"Kulkarni-Kale","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2023020210100916800_B9","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","author":"Larsen","year":"2006","journal-title":"Immunome Res"},{"key":"2023020210100916800_B10","doi-asserted-by":"crossref","first-page":"3789","DOI":"10.1093\/nar\/gkg620","article-title":"UniqueProt: creating representative protein-sequence sets","volume":"31","author":"Mika","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2023020210100916800_B11","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1002\/jmr.602","article-title":"BEPITOPE: predicting the location of continuous epitopes and patterns in proteins","volume":"16","author":"Odorico","year":"2003","journal-title":"J. Mol. Recognit"},{"key":"2023020210100916800_B12","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1002\/jmr.819","article-title":"Identification of discontinuous antigenic determinants on proteins based on shape complementarities","volume":"20","author":"Rapberger","year":"2007","journal-title":"J. Mol. Recognit"},{"key":"2023020210100916800_B13","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1002\/prot.21078","article-title":"Prediction of continuous B-cell epitopes in an antigen using recurrent neural networks","volume":"65","author":"Saha","year":"2006","journal-title":"Prot. Struct. Funct. Bioinform"},{"key":"2023020210100916800_B14","doi-asserted-by":"crossref","first-page":"D777","DOI":"10.1093\/nar\/gkj053","article-title":"Epitome: database of structure-inferred antigenic epitopes","volume":"34","author":"Schlessinger","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2023020210100916800_B15","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1006\/meth.1996.0054","article-title":"Mapping epitope structure and activity: from one-dimensional prediction to four-dimensional description of antigenic specificity","volume":"9","author":"van Regenmortel","year":"1996","journal-title":"Methods"},{"key":"2023020210100916800_B16","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1002\/jmr.768","article-title":"Immunoinformatics may lead to a reappraisal of the nature of B cell epitopes and of the feasibility of synthetic peptide vaccines","volume":"19","author":"van Regenmortel","year":"2006","journal-title":"J. Mol. Recognit"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/12\/1459\/49046222\/bioinformatics_24_12_1459.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/24\/12\/1459\/49046222\/bioinformatics_24_12_1459.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,2]],"date-time":"2023-02-02T11:44:11Z","timestamp":1675338251000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/24\/12\/1459\/195823"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,4,28]]},"references-count":16,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2008,6,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btn199","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2008,6,15]]},"published":{"date-parts":[[2008,4,28]]}}}