{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T02:03:24Z","timestamp":1773885804380,"version":"3.50.1"},"reference-count":57,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,10,21]],"date-time":"2021-10-21T00:00:00Z","timestamp":1634774400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Medical Research Council and Funda\u00e7\u00e3o de Amparo \u00e0 Pesquisa do Estado de Minas Gerais","award":["MR\/M026302\/1"],"award-info":[{"award-number":["MR\/M026302\/1"]}]},{"name":"National Health and Medical Research Council of Australia","award":["GNT1174405"],"award-info":[{"award-number":["GNT1174405"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The ability to identify antigenic determinants of pathogens, or epitopes, is fundamental to guide rational vaccine development and immunotherapies, which are particularly relevant for rapid pandemic response. A range of computational tools has been developed over the past two decades to assist in epitope prediction; however, they have presented limited performance and generalization, particularly for the identification of conformational B-cell epitopes. Here, we present epitope3D, a novel scalable machine learning method capable of accurately identifying conformational epitopes trained and evaluated on the largest curated epitope data set to date. Our method uses the concept of graph-based signatures to model epitope and non-epitope regions as graphs and extract distance patterns that are used as evidence to train and test predictive models. We show epitope3D outperforms available alternative approaches, achieving Mathew\u2019s Correlation Coefficient and F1-scores of 0.55 and 0.57 on cross-validation and 0.45 and 0.36 during independent blind tests, respectively.<\/jats:p>","DOI":"10.1093\/bib\/bbab423","type":"journal-article","created":{"date-parts":[[2021,9,16]],"date-time":"2021-09-16T11:10:35Z","timestamp":1631790635000},"source":"Crossref","is-referenced-by-count":73,"title":["epitope3D: a machine learning method for conformational B-cell epitope prediction"],"prefix":"10.1093","volume":"23","author":[{"given":"Bruna Moreira","family":"da Silva","sequence":"first","affiliation":[{"name":"Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia"},{"name":"School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia"}]},{"given":"YooChan","family":"Myung","sequence":"additional","affiliation":[{"name":"Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia"},{"name":"Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2948-2413","authenticated-orcid":false,"given":"David B","family":"Ascher","sequence":"additional","affiliation":[{"name":"Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia"},{"name":"Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Department of Biochemistry, University of Cambridge, 80 Tennis Ct Rd, Cambridge CB2 1GA, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3004-2119","authenticated-orcid":false,"given":"Douglas E V","family":"Pires","sequence":"additional","affiliation":[{"name":"Structural Biology and Bioinformatics, Department of Biochemistry, University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Systems and Computational Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia"},{"name":"Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia"},{"name":"School of Computing and Information Systems, University of Melbourne, Melbourne, Victoria, Australia"}]}],"member":"286","published-online":{"date-parts":[[2021,10,21]]},"reference":[{"key":"2022011921222465100_ref1","volume-title":"Roitt's Essential Immunology","author":"Delves","year":"2017"},{"key":"2022011921222465100_ref2","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-59745-450-6_1","volume-title":"What Is a B-Cell Epitope? 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