{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,30]],"date-time":"2026-08-30T12:44:10Z","timestamp":1788093850513,"version":"build-2803163510"},"reference-count":26,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,7,7]],"date-time":"2025-07-07T00:00:00Z","timestamp":1751846400000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Leading Medical Talents Program of Health Commission of Yunnan Province","award":["L-2018013"],"award-info":[{"award-number":["L-2018013"]}]},{"name":"Basic Research Program of Yunnan Province","award":["202201AU070152"],"award-info":[{"award-number":["202201AU070152"]}]},{"name":"Basic Research Program of Yunnan Province","award":["202101AS070051"],"award-info":[{"award-number":["202101AS070051"]}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2023YFC2307704"],"award-info":[{"award-number":["2023YFC2307704"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Science and Technology Plan-biological medical special project of Yunnan Province","award":["202302AA310005"],"award-info":[{"award-number":["202302AA310005"]}]},{"name":"CAMS Innovation Fund for Medical Sciences","award":["CIFMS, 2024-I2M-TS-030I, 2023-I2M-QJ-018"],"award-info":[{"award-number":["CIFMS, 2024-I2M-TS-030I, 2023-I2M-QJ-018"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Identifying B cell dominant epitopes helps to improve vaccine design and better understand immune evasion of pathogens. Herein, we present the Intelligent Batch Epitope Identification and Partitioning (IBEIP), an intelligent tool for identifying B cell dominant epitope regions based on antigen-neutralizing antibody (Ag-nAb) complex data. IBEIP can accurately map the epitopes on any appointed Ag-nAb complex by analyzing antigen\u2013antibody interactions at a molecular level. Combined with a hierarchical iterative merging model, IBEIP can intelligently merge and analyze mapped epitopes to identify B cell dominant epitopes. It is also applicable to analyzing high-mutant antigens and complex epitope structures. We demonstrated the performance of IBEIP by analyzing 127 Ag-nAb complexes from the respiratory syncytial virus (RSV) fusion, SARS-CoV-2 spike, and high-mutant influenza hemagglutinin. Over 90% of the residues overlapped between IBEIP and reported epitopes, confirming its reliability. IBEIP also uncovered new and important B cell dominant epitope regions and structures of these pathogens for researchers. Our study provides a reliable, intelligent tool for B cell dominant epitope analysis and offers some valuable insights for preventing RSV, SARS-CoV-2, and influenza infections.<\/jats:p>","DOI":"10.1093\/bib\/bbaf310","type":"journal-article","created":{"date-parts":[[2025,7,4]],"date-time":"2025-07-04T11:56:42Z","timestamp":1751630202000},"source":"Crossref","is-referenced-by-count":2,"title":["Intelligent Batch Epitope Identification and Partitioning: an intelligent tool for the identification of B cell dominant epitopes"],"prefix":"10.1093","volume":"26","author":[{"given":"Yun-Fei","family":"Ma","sequence":"first","affiliation":[{"name":"Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , No. 935, Jiaoling Road, Kunming, 650118 ,","place":["People\u2019s Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ye","family":"Liu","sequence":"additional","affiliation":[{"name":"Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College , No. 935, Jiaoling Road, Kunming, 650118 ,","place":["People\u2019s Republic of China"]},{"name":"State Key Laboratory of Respiratory Health and Multimorbidity , No. 9, Dongdan San Tiao, Beijing, 100190 ,","place":["People\u2019s Republic of China"]},{"name":"Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education , No. 9, Dongdan San Tiao, Beijing 100190 ,","place":["People\u2019s Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,7,7]]},"reference":[{"key":"2025070709544114600_ref1","doi-asserted-by":"publisher","first-page":"456","DOI":"10.1038\/ni.3680","article-title":"Defining B cell immunodominance to viruses","volume":"18","author":"Angeletti","year":"2017","journal-title":"Nat Immunol"},{"key":"2025070709544114600_ref2","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1006\/scbi.2001.0401","article-title":"Immunodominance and tumor escape","volume":"12","author":"Schreiber","year":"2002","journal-title":"Semin Cancer Biol"},{"key":"2025070709544114600_ref3","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1016\/j.scib.2023.12.021","article-title":"Rational design of a cross-type HPV vaccine through immunodominance shift guided by a cross-neutralizing antibody","volume":"69","author":"Wang","year":"2024","journal-title":"Sci Bull (Beijing)"},{"key":"2025070709544114600_ref4","doi-asserted-by":"publisher","first-page":"2670","DOI":"10.1080\/22221751.2022.2135460","article-title":"Immunodominance hierarchy after seasonal influenza vaccination","volume":"11","author":"Sanchez-de Prada","year":"2022","journal-title":"Emerg Microbes Infect"},{"key":"2025070709544114600_ref5","doi-asserted-by":"publisher","first-page":"112262","DOI":"10.1016\/j.celrep.2023.112262","article-title":"Immunodominant surface epitopes power immune evasion in the African trypanosome","volume":"42","author":"Gkeka","year":"2023","journal-title":"Cell Rep"},{"key":"2025070709544114600_ref6","doi-asserted-by":"publisher","first-page":"1290","DOI":"10.1016\/j.immuni.2021.05.001","article-title":"Profiling B cell immunodominance after SARS-CoV-2 infection reveals antibody evolution to non-neutralizing viral targets","volume":"54","author":"Dugan","year":"2021","journal-title":"Immunity"},{"key":"2025070709544114600_ref7","doi-asserted-by":"publisher","first-page":"1415","DOI":"10.1053\/j.gastro.2024.08.015","article-title":"Crohn\u2019s patients and healthy infants share immunodominant B cell response to commensal flagellin peptide epitopes","volume":"167","author":"Zhao","year":"2024","journal-title":"Gastroenterology"},{"key":"2025070709544114600_ref8","doi-asserted-by":"publisher","first-page":"980","DOI":"10.1038\/nsb1203-980","article-title":"Announcing the worldwide protein data Bank","volume":"10","author":"Berman","year":"2003","journal-title":"Nat Struct Biol"},{"key":"2025070709544114600_ref9","doi-asserted-by":"publisher","first-page":"1024","DOI":"10.1016\/j.cell.2020.09.037","article-title":"Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology","volume":"183","author":"Piccoli","year":"2020","journal-title":"Cell"},{"key":"2025070709544114600_ref10","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1038\/s41467-020-20602-5","article-title":"A therapeutic neutralizing antibody targeting receptor binding domain of SARS-CoV-2 spike protein","volume":"12","author":"Kim","year":"2021","journal-title":"Nat Commun"},{"key":"2025070709544114600_ref11","doi-asserted-by":"publisher","first-page":"728","DOI":"10.1126\/science.abq3773","article-title":"Broadly neutralizing antibodies target the coronavirus fusion peptide","volume":"377","author":"Dacon","year":"2022","journal-title":"Science"},{"key":"2025070709544114600_ref12","doi-asserted-by":"publisher","first-page":"1693","DOI":"10.1016\/j.immuni.2022.07.006","article-title":"Allelic polymorphism controls autoreactivity and vaccine elicitation of human broadly neutralizing antibodies against influenza virus","volume":"55","author":"Sangesland","year":"2022","journal-title":"Immunity"},{"key":"2025070709544114600_ref13","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1016\/B978-0-12-381270-4.00019-6","article-title":"ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules","volume":"487","author":"Leaver-Fay","year":"2011","journal-title":"Methods Enzymol"},{"key":"2025070709544114600_ref14","doi-asserted-by":"publisher","first-page":"1653","DOI":"10.1111\/all.13398","article-title":"Similar localization of conformational IgE epitopes on the house dust mite allergens Der p 5 and Der p 21 despite limited IgE cross-reactivity","volume":"73","author":"Curin","year":"2018","journal-title":"Allergy"},{"key":"2025070709544114600_ref15","doi-asserted-by":"publisher","first-page":"1227","DOI":"10.3390\/vaccines10081227","article-title":"The relative positioning of B and T cell epitopes drives immunodominance","volume":"10","author":"Biavasco","year":"2022","journal-title":"Vaccines (Basel)"},{"key":"2025070709544114600_ref16","doi-asserted-by":"crossref","first-page":"eadc9498","DOI":"10.1126\/science.adc9498","article-title":"Germline-encoded amino acid-binding motifs drive immunodominant public antibody responses","volume":"380","author":"Shrock","year":"2023","journal-title":"Science"},{"key":"2025070709544114600_ref17","doi-asserted-by":"publisher","first-page":"3022","DOI":"10.1093\/molbev\/msab120","article-title":"MEGA11: molecular evolutionary genetics analysis version 11","volume":"38","author":"Tamura","year":"2021","journal-title":"Mol Biol Evol"},{"key":"2025070709544114600_ref18","doi-asserted-by":"publisher","first-page":"209","DOI":"10.1016\/j.tim.2017.09.009","article-title":"Clinical potential of prefusion RSV F-specific antibodies","volume":"26","author":"Rossey","year":"2018","journal-title":"Trends Microbiol"},{"key":"2025070709544114600_ref19","doi-asserted-by":"publisher","first-page":"3936","DOI":"10.1016\/j.cell.2021.06.005","article-title":"SARS-CoV-2 mRNA vaccination induces functionally diverse antibodies to NTD, RBD, and S2","volume":"184","author":"Amanat","year":"2021","journal-title":"Cell"},{"key":"2025070709544114600_ref20","doi-asserted-by":"crossref","first-page":"2447615","DOI":"10.1080\/22221751.2024.2447615","article-title":"Enhanced antibody response to the conformational non-RBD region via DNA prime-protein boost elicits broad cross-neutralization against SARS-CoV-2 variants","volume":"14","author":"Ma","year":"2025","journal-title":"Emerg Microbes Infect"},{"key":"2025070709544114600_ref21","doi-asserted-by":"publisher","first-page":"20210082","DOI":"10.1002\/EXP.20210082","article-title":"Nanotechnology-facilitated vaccine development during the coronavirus disease 2019 (COVID-19) pandemic","volume":"2","author":"Ziqi","year":"2022","journal-title":"Exploration (Beijing)"},{"key":"2025070709544114600_ref22","doi-asserted-by":"publisher","first-page":"e12024","DOI":"10.1002\/bmm2.12024","article-title":"Aptamer-based strategies against SARS-CoV-2 viruses","volume":"1","author":"Huang","year":"2023","journal-title":"BioMedical Engineering Materials"},{"key":"2025070709544114600_ref23","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1038\/s41579-021-00573-0","article-title":"SARS-CoV-2 variants, spike mutations and immune escape","volume":"19","author":"Harvey","year":"2021","journal-title":"Nat Rev Microbiol"},{"key":"2025070709544114600_ref24","doi-asserted-by":"publisher","first-page":"2332","DOI":"10.1016\/j.cell.2021.03.028","article-title":"N-terminal domain antigenic mapping reveals a site of vulnerability for SARS-CoV-2","volume":"184","author":"McCallum","year":"2021","journal-title":"Cell"},{"key":"2025070709544114600_ref25","doi-asserted-by":"publisher","first-page":"998","DOI":"10.1016\/j.immuni.2022.04.003","article-title":"Analysis of memory B cells identifies conserved neutralizing epitopes on the N-terminal domain of variant SARS-Cov-2 spike proteins","volume":"55","author":"Wang","year":"2022","journal-title":"Immunity"},{"key":"2025070709544114600_ref26","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1126\/science.abm0271","article-title":"A multivalent nucleoside-modified mRNA vaccine against all known influenza virus subtypes","volume":"378","author":"Arevalo","year":"2022","journal-title":"Science"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/4\/bbaf310\/63688255\/bbaf310.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/4\/bbaf310\/63688255\/bbaf310.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,7,7]],"date-time":"2025-07-07T13:54:49Z","timestamp":1751896489000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaf310\/8190207"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7]]},"references-count":26,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2025,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaf310","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,7]]},"published":{"date-parts":[[2025,7]]},"article-number":"bbaf310"}}