{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,29]],"date-time":"2026-01-29T01:30:50Z","timestamp":1769650250939,"version":"3.49.0"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T00:00:00Z","timestamp":1768262400000},"content-version":"vor","delay-in-days":12,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"General Research Fund","award":["14306324"],"award-info":[{"award-number":["14306324"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Accurate in silico identification of B-cell epitope residues is crucial for antibody design and structure-guided vaccine development. Although recent protein language models and structure-aware methods can capture spatial information of tertiary structure when generating residue embeddings, most existing epitope predictors use these embeddings to perform classification for individual residues one by one, without enforcing spatial continuity for reported epitope residues. Such methods often result in biologically implausible predictions because B-cell epitope residues always cluster together on the antigen surface.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present RoBep, a region-oriented B-cell epitope predictor that explicitly models the spatial clustering of epitope residues. RoBep introduces a novel region constraint mechanism and combines the advanced protein language model ESM-Cambrian with an equivariant graph neural network. Our method outperforms existing structure-based methods on the benchmark dataset, demonstrating improvements of 26%, 45%, 13%, and 43% in F1, Matthews correlation coefficient, area under the precision\u2013recall curve, and AUROC0.1, respectively. In addition to residue-level predictions, RoBep can also provide antibody\u2013antigen binding regions. Importantly, the predicted epitope residues are ensured to be spatially compact, enhancing biological plausibility and practical relevance for immunotherapeutic design.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>A user-friendly website for using RoBep is provided at https:\/\/huggingface.co\/spaces\/NielTT\/RoBep. All datasets, source code used in this work, and implementation instructions of the website are publicly available at https:\/\/github.com\/YitaoXU\/RoBep.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag006","type":"journal-article","created":{"date-parts":[[2026,1,7]],"date-time":"2026-01-07T12:41:29Z","timestamp":1767789689000},"source":"Crossref","is-referenced-by-count":0,"title":["RoBep: a region-oriented deep learning model for B-cell epitope prediction"],"prefix":"10.1093","volume":"42","author":[{"given":"Yitao","family":"Xu","sequence":"first","affiliation":[{"name":"Department of Statistics and Data Science, The Chinese University of Hong Kong , Shatin, N.T. , Hong Kong SAR,","place":["China"]}]},{"given":"Guanyun","family":"Wei","sequence":"additional","affiliation":[{"name":"School of Life Science, Nantong University , Nantong, Jiangsu, 226019,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9740-6159","authenticated-orcid":false,"given":"Jingying","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Biomedical Sciences, The Chinese University of Hong Kong , Shatin, N.T. , Hong Kong SAR,","place":["China"]}]},{"given":"Yuanhua","family":"Huang","sequence":"additional","affiliation":[{"name":"School of Biomedical Sciences, The University of Hong Kong , Pokfulam, Hong Kong, Hong Kong SAR,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5510-6916","authenticated-orcid":false,"given":"Weichuan","family":"Yu","sequence":"additional","affiliation":[{"name":"Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology , Hong Kong SAR,","place":["China"]}]},{"given":"Zhixiang","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Statistics and Data Science, The Chinese University of Hong Kong , Shatin, N.T. , Hong Kong SAR,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3627-3994","authenticated-orcid":false,"given":"Ran","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Statistics, Faculty of Arts and Sciences, Beijing Normal University , Zhuhai, Guangdong, 519087,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2744-9030","authenticated-orcid":false,"given":"Xiaodan","family":"Fan","sequence":"additional","affiliation":[{"name":"Department of Statistics and Data Science, The Chinese University of Hong Kong , Shatin, N.T. , Hong Kong SAR,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2026,1,12]]},"reference":[{"key":"2026012807260255500_btag006-B1","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1038\/322747a0","article-title":"Continuous and discontinuous protein antigenic 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