{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T15:34:48Z","timestamp":1789659288211,"version":"4.0.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Antibody epitope mapping is a key step in understanding antibody\u2013antigen recognition and is of particular interest for drug development, diagnostics and vaccine design. Most computational methods for epitope prediction are based on properties of the antigen sequence and\/or structure, not taking into account the antibody for which the epitope is predicted. Here, we introduce PEASE, a web server predicting antibody-specific epitopes, utilizing the sequence of the antibody. The predictions are provided both at the residue level and as patches on the antigen structure. The tradeoff between recall and precision can be tuned by the user, by changing the default parameters. The results are provided as text and HTML files as well as a graph, and can be viewed on the antigen 3D structure.<\/jats:p>\n               <jats:p>Availability and implementation: PEASE is freely available on the web at www.ofranlab.org\/PEASE.<\/jats:p>\n               <jats:p>Contact: \u00a0yanay@ofranlab.org<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu790","type":"journal-article","created":{"date-parts":[[2014,11,29]],"date-time":"2014-11-29T02:15:47Z","timestamp":1417227347000},"page":"1313-1315","source":"Crossref","is-referenced-by-count":70,"title":["PEASE: predicting B-cell epitopes utilizing antibody sequence"],"prefix":"10.1093","volume":"31","author":[{"given":"Inbal","family":"Sela-Culang","sequence":"first","affiliation":[{"name":"1 The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar-Ilan University, Ramat-Gan 52900, Israel and 2Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shaul","family":"Ashkenazi","sequence":"additional","affiliation":[{"name":"1 The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar-Ilan University, Ramat-Gan 52900, Israel and 2Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bjoern","family":"Peters","sequence":"additional","affiliation":[{"name":"1 The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar-Ilan University, Ramat-Gan 52900, Israel and 2Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanay","family":"Ofran","sequence":"additional","affiliation":[{"name":"1 The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar-Ilan University, Ramat-Gan 52900, Israel and 2Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2014,11,27]]},"reference":[{"key":"2023051309015368100_btu790-B1","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1007\/978-1-4939-1115-8_19","article-title":"T-cell epitope prediction methods: an overview","volume":"1184","author":"Desai","year":"2014","journal-title":"Methods Mol. Biol."},{"key":"2023051309015368100_btu790-B2","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1002\/jmr.815","article-title":"Towards 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":"2023051309015368100_btu790-B3","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","author":"Krawczyk","year":"2014","journal-title":"Bioinformatics"},{"key":"2023051309015368100_btu790-B4","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","author":"Kringelum","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"2023051309015368100_btu790-B5","first-page":"43","article-title":"Predictions versus high-throughput experiments in T-cell epitope discovery: competition or synergy? Expert Rev","volume":"11","author":"Lundegaard","year":"2012","journal-title":"Vaccines"},{"key":"2023051309015368100_btu790-B6","doi-asserted-by":"crossref","first-page":"302","DOI":"10.3389\/fimmu.2013.00302","article-title":"The structural basis of antibody-antigen recognition","volume":"4","author":"Sela-Culang","year":"2013","journal-title":"Front Immunol."},{"key":"2023051309015368100_btu790-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","author":"Sela-Culang","year":"2014","journal-title":"Structure"},{"key":"2023051309015368100_btu790-B8","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1093\/protein\/gzq014","article-title":"Use of amino acid composition to predict epitope residues of individual antibodies","volume":"23","author":"Soga","year":"2010","journal-title":"Protein Eng. Des. Sel."},{"key":"2023051309015368100_btu790-B9","doi-asserted-by":"crossref","first-page":"2169","DOI":"10.1007\/s11434-010-3199-z","article-title":"Evaluation of spatial epitope computational tools based on experimentally-confirmed dataset for protein antigens","volume":"55","author":"Xu","year":"2010","journal-title":"Chin. Sci. Bull."},{"key":"2023051309015368100_btu790-B10","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1002\/rmv.602","article-title":"An introduction to epitope prediction methods and software","volume":"19","author":"Yang","year":"2009","journal-title":"Rev. Med. Virol."},{"key":"2023051309015368100_btu790-B11","doi-asserted-by":"crossref","first-page":"e62249","DOI":"10.1371\/journal.pone.0062249","article-title":"Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods","volume":"8","author":"Yao","year":"2013","journal-title":"PLoS One"},{"key":"2023051309015368100_btu790-B12","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1186\/1472-6807-10-S1-S6","article-title":"Mining for the antibody-antigen interacting associations that predict the B cell epitopes","volume":"10","author":"Zhao","year":"2010","journal-title":"BMC Struct. Biol."},{"key":"2023051309015368100_btu790-B13","doi-asserted-by":"crossref","first-page":"1483","DOI":"10.1109\/TCBB.2011.49","article-title":"Antibody-specified B-cell epitope prediction in line with the principle of context-awareness","volume":"8","author":"Zhao","year":"2011","journal-title":"IEEE-ACM Trans. Comput. Biol. Bioinform."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/8\/1313\/50306135\/bioinformatics_31_8_1313.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/31\/8\/1313\/50306135\/bioinformatics_31_8_1313.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,13]],"date-time":"2023-05-13T09:02:11Z","timestamp":1683968531000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/31\/8\/1313\/212227"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,11,27]]},"references-count":13,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2015,4,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btu790","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2015,4,15]]},"published":{"date-parts":[[2014,11,27]]}}}