{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T02:53:22Z","timestamp":1770692002928,"version":"3.49.0"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,22]],"date-time":"2023-05-22T00:00:00Z","timestamp":1684713600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2019YFA0905900"],"award-info":[{"award-number":["2019YFA0905900"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32070657"],"award-info":[{"award-number":["32070657"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81830080"],"award-info":[{"award-number":["81830080"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31900483"],"award-info":[{"award-number":["31900483"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Sailing Program","award":["19YF1441100"],"award-info":[{"award-number":["19YF1441100"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Identifying the exact epitope positions for a monoclonal antibody (mAb) is of critical importance yet highly challenging to the Ab design of biomedical research. Based on previous versions of SEPPA 3.0, we present SEPPA-mAb for the above purpose with high accuracy and low false positive rate (FPR), suitable for both experimental and modelled structures. In practice, SEPPA-mAb appended a fingerprints-based patch model to SEPPA 3.0, considering the structural and physic-chemical complementarity between a possible epitope patch and the complementarity-determining region of mAb and trained on 860 representative antigen-antibody complexes. On independent testing of 193 antigen-antibody pairs, SEPPA-mAb achieved an accuracy of 0.873 with an FPR of 0.097 in classifying epitope and non-epitope residues under the default threshold, while docking-based methods gave the best AUC of 0.691, and the top epitope prediction tool gave AUC of 0.730 with balanced accuracy of 0.635. A study on 36 independent HIV glycoproteins displayed a high accuracy of 0.918 and a low FPR of 0.058. Further testing illustrated outstanding robustness on new antigens and modelled antibodies. Being the first online tool predicting mAb-specific epitopes, SEPPA-mAb may help to discover new epitopes and design better mAbs for therapeutic and diagnostic purposes. SEPPA-mAb can be accessed at http:\/\/www.badd-cao.net\/seppa-mab\/.<\/jats:p>","DOI":"10.1093\/nar\/gkad427","type":"journal-article","created":{"date-parts":[[2023,5,22]],"date-time":"2023-05-22T19:32:51Z","timestamp":1684783971000},"page":"W528-W534","source":"Crossref","is-referenced-by-count":20,"title":["SEPPA-mAb: spatial epitope prediction of protein antigens for mAbs"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2619-0298","authenticated-orcid":false,"given":"Tianyi","family":"Qiu","sequence":"first","affiliation":[{"name":"School of Life Sciences, Fudan University , Shanghai \u00a0200092, China"},{"name":"Institute of Clinical Science, Zhongshan Hospital, Fudan University , Shanghai \u00a0200032, China"}]},{"given":"Lu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5430-6596","authenticated-orcid":false,"given":"Zikun","family":"Chen","sequence":"additional","affiliation":[{"name":"Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092, China"}]},{"given":"Yuan","family":"Wang","sequence":"additional","affiliation":[{"name":"Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092, China"}]},{"given":"Tiantian","family":"Mao","sequence":"additional","affiliation":[{"name":"Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092, China"}]},{"given":"Caicui","family":"Wang","sequence":"additional","affiliation":[{"name":"Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092, China"}]},{"given":"Yewei","family":"Cun","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Fudan University , Shanghai \u00a0200092, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5380-2435","authenticated-orcid":false,"given":"Genhui","family":"Zheng","sequence":"additional","affiliation":[{"name":"Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0511-1423","authenticated-orcid":false,"given":"Deyu","family":"Yan","sequence":"additional","affiliation":[{"name":"Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092, China"}]},{"given":"Mengdi","family":"Zhou","sequence":"additional","affiliation":[{"name":"Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0508-6056","authenticated-orcid":false,"given":"Kailin","family":"Tang","sequence":"additional","affiliation":[{"name":"Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092, China"}]},{"given":"Zhiwei","family":"Cao","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Fudan University , Shanghai \u00a0200092, China"},{"name":"Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University , Shanghai \u00a0200092, China"}]}],"member":"286","published-online":{"date-parts":[[2023,5,22]]},"reference":[{"key":"2023070505010969100_B1","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.tibtech.2018.05.014","article-title":"The increasingly human and profitable monoclonal antibody market","volume":"37","author":"Grilo","year":"2019","journal-title":"Trends Biotechnol."},{"key":"2023070505010969100_B2","doi-asserted-by":"crossref","first-page":"101427","DOI":"10.1016\/j.smim.2020.101427","article-title":"Quantum leap of monoclonal antibody (mAb) discovery and development in the COVID-19 era","volume":"50","author":"Pecetta","year":"2020","journal-title":"Semin. 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