{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T18:56:27Z","timestamp":1768589787991,"version":"3.49.0"},"reference-count":85,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,4,23]],"date-time":"2024-04-23T00:00:00Z","timestamp":1713830400000},"content-version":"vor","delay-in-days":27,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Zhejiang Provincial Natural Science Foundation of China","award":["LDT23H19011H19"],"award-info":[{"award-number":["LDT23H19011H19"]}]},{"name":"Zhejiang Provincial Natural Science Foundation of China","award":["LHDMZ22H300002"],"award-info":[{"award-number":["LHDMZ22H300002"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31971371"],"award-info":[{"award-number":["31971371"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"K.P. Chao\u2019s High Technology Development Foundation of Zhejiang University","award":["2022RC018"],"award-info":[{"award-number":["2022RC018"]}]},{"DOI":"10.13039\/501100004835","name":"Zhejiang University","doi-asserted-by":"publisher","award":["XY2022038"],"award-info":[{"award-number":["XY2022038"]}],"id":[{"id":"10.13039\/501100004835","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Coronaviruses have threatened humans repeatedly, especially COVID-19 caused by SARS-CoV-2, which has posed a substantial threat to global public health. SARS-CoV-2 continuously evolves through random mutation, resulting in a significant decrease in the efficacy of existing vaccines and neutralizing antibody drugs. It is critical to assess immune escape caused by viral mutations and develop broad-spectrum vaccines and neutralizing antibodies targeting conserved epitopes. Thus, we constructed CovEpiAb, a comprehensive database and analysis resource of human coronavirus (HCoVs) immune epitopes and antibodies. CovEpiAb contains information on over 60\u00a0000 experimentally validated epitopes and over 12\u00a0000 antibodies for HCoVs and SARS-CoV-2 variants. The database is unique in (1) classifying and annotating cross-reactive epitopes from different viruses and variants; (2) providing molecular and experimental interaction profiles of antibodies, including structure-based binding sites and around 70\u00a0000 data on binding affinity and neutralizing activity; (3) providing virological characteristics of current and past circulating SARS-CoV-2 variants and in vitro activity of various therapeutics; and (4) offering site-level annotations of key functional features, including antibody binding, immunological epitopes, SARS-CoV-2 mutations and conservation across HCoVs. In addition, we developed an integrated pipeline for epitope prediction named COVEP, which is available from the webpage of CovEpiAb. CovEpiAb is freely accessible at https:\/\/pgx.zju.edu.cn\/covepiab\/.<\/jats:p>","DOI":"10.1093\/bib\/bbae183","type":"journal-article","created":{"date-parts":[[2024,4,23]],"date-time":"2024-04-23T09:55:52Z","timestamp":1713866152000},"source":"Crossref","is-referenced-by-count":4,"title":["CovEpiAb: a comprehensive database and analysis resource for immune epitopes and antibodies of human coronaviruses"],"prefix":"10.1093","volume":"25","author":[{"given":"Xue","family":"Zhang","sequence":"first","affiliation":[{"name":"National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"JingCheng","family":"Wu","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuanyuan","family":"Luo","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yilin","family":"Wang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yujie","family":"Wu","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaobin","family":"Xu","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yufang","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruiying","family":"Kong","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ying","family":"Chi","sequence":"additional","affiliation":[{"name":"Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou 310058 , China"},{"name":"ZJU-UoE Institute, Zhejiang University , Haining 314400 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yisheng","family":"Sun","sequence":"additional","affiliation":[{"name":"Key Lab of Vaccine , Prevention and Control of Infectious Disease of Zhejiang Province, , Hangzhou 310015 , China"},{"name":"Zhejiang Provincial Center for Disease Control and Prevention , Prevention and Control of Infectious Disease of Zhejiang Province, , Hangzhou 310015 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuqing","family":"Chen","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiaojun","family":"He","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University Innovation Institute for Artificial Intelligence in Medicine , Engineering Research Center of Innovative Anticancer Drugs, , Hangzhou 310018 , China"},{"name":"Ministry of Education , Engineering Research Center of Innovative Anticancer Drugs, , Hangzhou 310018 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8069-0053","authenticated-orcid":false,"given":"Feng","family":"Zhu","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University Innovation Institute for Artificial Intelligence in Medicine , Engineering Research Center of Innovative Anticancer Drugs, , Hangzhou 310018 , China"},{"name":"Ministry of Education , Engineering Research Center of Innovative Anticancer Drugs, , Hangzhou 310018 , China"},{"name":"Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou 310058 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2730-5483","authenticated-orcid":false,"given":"Zhan","family":"Zhou","sequence":"additional","affiliation":[{"name":"National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University , College of Pharmaceutical Sciences, , Hangzhou 310058 , China"},{"name":"Zhejiang University Innovation Institute for Artificial Intelligence in Medicine , Engineering Research Center of Innovative Anticancer Drugs, , Hangzhou 310018 , China"},{"name":"Ministry of Education , Engineering Research Center of Innovative Anticancer Drugs, , Hangzhou 310018 , China"},{"name":"Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare , Hangzhou 310058 , China"},{"name":"The Fourth Affiliated Hospital, Zhejiang University School of Medicine , Yiwu 322000 , China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,4,22]]},"reference":[{"issue":"7798","key":"2024042309553826100_ref1","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","article-title":"A pneumonia outbreak associated with a new coronavirus of probable bat origin","volume":"579","author":"Zhou","year":"2020","journal-title":"Nature"},{"key":"2024042309553826100_ref2"},{"issue":"7923","key":"2024042309553826100_ref3","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1038\/s41586-022-04980-y","article-title":"BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by omicron infection","volume":"608","author":"Cao","year":"2022","journal-title":"Nature"},{"issue":"7857","key":"2024042309553826100_ref4","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1038\/s41586-021-03398-2","article-title":"Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7","volume":"593","author":"Wang","year":"2021","journal-title":"Nature"},{"issue":"2","key":"2024042309553826100_ref5","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1016\/j.cell.2022.12.018","article-title":"Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants","volume":"186","author":"Wang","year":"2023","journal-title":"Cell"},{"issue":"7","key":"2024042309553826100_ref6","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1056\/NEJMc2214314","article-title":"Substantial neutralization escape by SARS-CoV-2 omicron variants BQ.1.1 and XBB.1","volume":"388","author":"Miller","year":"2023","journal-title":"N Engl J Med"},{"issue":"14","key":"2024042309553826100_ref7","doi-asserted-by":"crossref","first-page":"2422","DOI":"10.1016\/j.cell.2022.06.005","article-title":"Antibody escape of SARS-CoV-2 omicron BA.4 and BA.5 from vaccine and BA.1 serum","volume":"185","author":"Tuekprakhon","year":"2022","journal-title":"Cell"},{"issue":"2","key":"2024042309553826100_ref8","doi-asserted-by":"crossref","first-page":"344","DOI":"10.1038\/s41591-022-02162-x","article-title":"Low neutralization of SARS-CoV-2 omicron BA.2.75.2, BQ.1.1 and XBB.1 by parental mRNA vaccine or a BA.5 bivalent booster","volume":"29","author":"Kurhade","year":"2023","journal-title":"Nat Med"},{"issue":"9","key":"2024042309553826100_ref9","doi-asserted-by":"crossref","first-page":"2372","DOI":"10.1016\/j.cell.2021.03.013","article-title":"Multiple SARS-CoV-2 variants escape neutralization by vaccine-induced humoral immunity","volume":"184","author":"Garcia-Beltran","year":"2021","journal-title":"Cell"},{"key":"2024042309553826100_ref10","article-title":"Anti-SARS-CoV-2 monoclonal antibodies. COVID-19 treatment guidelines"},{"issue":"7","key":"2024042309553826100_ref11","doi-asserted-by":"crossref","first-page":"942","DOI":"10.1016\/S1473-3099(22)00365-6","article-title":"Neutralisation sensitivity of SARS-CoV-2 omicron subvariants to therapeutic monoclonal antibodies","volume":"22","author":"Yamasoba","year":"2022","journal-title":"Lancet Infect Dis"},{"issue":"8","key":"2024042309553826100_ref12","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/nrmicro.2016.81","article-title":"SARS and MERS: recent insights into emerging coronaviruses","volume":"14","author":"Wit","year":"2016","journal-title":"Nat Rev Microbiol"},{"issue":"3","key":"2024042309553826100_ref13","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1038\/nrmicro775","article-title":"SARS\u2014beginning to understand a new virus","volume":"1","author":"Stadler","year":"2003","journal-title":"Nat Rev Microbiol"},{"issue":"6485","key":"2024042309553826100_ref14","doi-asserted-by":"crossref","first-page":"1444","DOI":"10.1126\/science.abb2762","article-title":"Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2","volume":"367","author":"Yan","year":"2020","journal-title":"Science"},{"issue":"2","key":"2024042309553826100_ref15","doi-asserted-by":"crossref","DOI":"10.1002\/rmv.2282","article-title":"An overview on the seven pathogenic human coronaviruses","volume":"32","author":"Kesheh","year":"2022","journal-title":"Rev Med Virol"},{"issue":"8","key":"2024042309553826100_ref16","doi-asserted-by":"crossref","first-page":"1701","DOI":"10.1016\/j.mayocp.2020.05.032","article-title":"Seasonality of coronavirus 229E, HKU1, NL63, and OC43 from 2014 to 2020","volume":"95","author":"Rucinski","year":"2020","journal-title":"Mayo Clin Proc"},{"issue":"6564","key":"2024042309553826100_ref17","doi-asserted-by":"crossref","first-page":"eabh1823","DOI":"10.1126\/science.abh1823","article-title":"Cross-reactive CD4+ T cells enhance SARS-CoV-2 immune responses upon infection and vaccination","volume":"374","author":"Loyal","year":"2021","journal-title":"Science"},{"issue":"1","key":"2024042309553826100_ref18","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1038\/s41467-021-27674-x","article-title":"Cross-reactive memory T cells associate with protection against SARS-CoV-2 infection in COVID-19 contacts","volume":"13","author":"Kundu","year":"2022","journal-title":"Nat Commun"},{"issue":"7821","key":"2024042309553826100_ref19","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/s41586-020-2550-z","article-title":"SARS-CoV-2-specific T cell immunity in cases of COVID-19 and SARS, and uninfected controls","volume":"584","author":"Le Bert","year":"2020","journal-title":"Nature"},{"issue":"1","key":"2024042309553826100_ref20","doi-asserted-by":"crossref","first-page":"bbab496","DOI":"10.1093\/bib\/bbab496","article-title":"Immuno-informatics analysis predicts B and T cell consensus epitopes for designing peptide vaccine against SARS-CoV-2 with 99.82% global population coverage","volume":"23","author":"Shukla","year":"2022","journal-title":"Brief Bioinform"},{"issue":"7","key":"2024042309553826100_ref21","first-page":"1622","article-title":"Prediction of conserved HLA class I and class II epitopes from SARS-CoV-2 licensed vaccines supports T-cell cross-protection against SARS-CoV-1","volume":"10","author":"L\u00f3pez","year":"2022","journal-title":"Biomedicine"},{"issue":"6","key":"2024042309553826100_ref22","doi-asserted-by":"crossref","first-page":"2977","DOI":"10.3390\/ijms23062977","article-title":"Cross-recognition of SARS-CoV-2 B-cell epitopes with other Betacoronavirus nucleoproteins","volume":"23","author":"Tajuelo","year":"2022","journal-title":"Int J Mol Sci"},{"issue":"15","key":"2024042309553826100_ref23","doi-asserted-by":"crossref","first-page":"1401","DOI":"10.1056\/NEJMoa2108453","article-title":"Pan-Sarbecovirus neutralizing antibodies in BNT162b2-immunized SARS-CoV-1 survivors","volume":"385","author":"Tan","year":"2021","journal-title":"N Engl J Med"},{"issue":"6607","key":"2024042309553826100_ref24","doi-asserted-by":"crossref","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"},{"issue":"13","key":"2024042309553826100_ref25","doi-asserted-by":"crossref","first-page":"30494","DOI":"10.2807\/1560-7917.ES.2017.22.13.30494","article-title":"GISAID: global initiative on sharing all influenza data\u2014from vision to reality","volume":"22","author":"Shu","year":"2017","journal-title":"Euro Surveill"},{"issue":"D1","key":"2024042309553826100_ref26","doi-asserted-by":"crossref","first-page":"D20","DOI":"10.1093\/nar\/gkab1112","article-title":"Database resources of the national center for biotechnology information","volume":"50","author":"Sayers","year":"2022","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"2024042309553826100_ref27","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1016\/j.gpb.2020.09.001","article-title":"The global landscape of SARS-CoV-2 genomes, variants, and haplotypes in 2019nCoVR","volume":"18","author":"Song","year":"2020","journal-title":"Genomics Proteomics Bioinformatics"},{"issue":"23","key":"2024042309553826100_ref28","doi-asserted-by":"crossref","first-page":"4121","DOI":"10.1093\/bioinformatics\/bty407","article-title":"Nextstrain: real-time tracking of pathogen evolution","volume":"34","author":"Hadfield","year":"2018","journal-title":"Bioinformatics"},{"key":"2024042309553826100_ref29","first-page":"121","article-title":"Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351\/501Y-V2 with grinch","volume":"6","author":"O\u2019Toole","year":"2021","journal-title":"Wellcome Open Res"},{"issue":"2","key":"2024042309553826100_ref30","doi-asserted-by":"crossref","first-page":"veab092","DOI":"10.1093\/ve\/veab092","article-title":"CoVizu: rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes","volume":"7","author":"Ferreira","year":"2021","journal-title":"Virus Evol"},{"issue":"4","key":"2024042309553826100_ref31","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1038\/s41592-023-01770-w","article-title":"Outbreak.info research library: a standardized, searchable platform to discover and explore COVID-19 resources","volume":"20","author":"Tsueng","year":"2023","journal-title":"Nat Methods"},{"issue":"D1","key":"2024042309553826100_ref32","doi-asserted-by":"crossref","first-page":"D817","DOI":"10.1093\/nar\/gkaa846","article-title":"ViruSurf: an integrated database to investigate viral sequences","volume":"49","author":"Canakoglu","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2024042309553826100_ref33","doi-asserted-by":"crossref","first-page":"D706","DOI":"10.1093\/nar\/gkaa808","article-title":"GESS: a database of global evaluation of SARS-CoV-2\/hCoV-19 sequences","volume":"49","author":"Fang","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"2024042309553826100_ref34","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0261045","article-title":"Coronavirus resistance database (CoV-RDB): SARS-CoV-2 susceptibility to monoclonal antibodies, convalescent plasma, and plasma from vaccinated persons","volume":"17","author":"Tzou","year":"2022","journal-title":"PloS One"},{"issue":"D1","key":"2024042309553826100_ref35","doi-asserted-by":"crossref","first-page":"D888","DOI":"10.1093\/nar\/gkab921","article-title":"VarEPS: an evaluation and prewarning system of known and virtual variations of SARS-CoV-2 genomes","volume":"50","author":"Sun","year":"2022","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2024042309553826100_ref36","doi-asserted-by":"crossref","first-page":"D282","DOI":"10.1093\/nar\/gkaa731","article-title":"CoV3D: a database of high resolution coronavirus protein structures","volume":"49","author":"Gowthaman","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2024042309553826100_ref37","doi-asserted-by":"crossref","DOI":"10.3389\/fphar.2020.572249","article-title":"COVIEdb: a database for potential immune epitopes of coronaviruses","volume":"11","author":"Wu","year":"2020","journal-title":"Front Pharmacol"},{"issue":"5","key":"2024042309553826100_ref38","doi-asserted-by":"crossref","first-page":"734","DOI":"10.1093\/bioinformatics\/btaa739","article-title":"CoV-AbDab: the coronavirus antibody database","volume":"37","author":"Raybould","year":"2021","journal-title":"Bioinformatics"},{"issue":"16","key":"2024042309553826100_ref39","doi-asserted-by":"crossref","first-page":"4051","DOI":"10.1093\/bioinformatics\/btac439","article-title":"Ab-CoV: a curated database for binding affinity and neutralization profiles of coronavirus-related antibodies","volume":"38","author":"Rawat","year":"2022","journal-title":"Bioinformatics"},{"issue":"D1","key":"2024042309553826100_ref40","doi-asserted-by":"crossref","first-page":"D589","DOI":"10.1093\/nar\/gkaa1094","article-title":"PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies","volume":"49","author":"Yue","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2024042309553826100_ref41","doi-asserted-by":"crossref","first-page":"D546","DOI":"10.1093\/nar\/gkac834","article-title":"CovInter: interaction data between coronavirus RNAs and host proteins","volume":"51","author":"Amahong","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2024042309553826100_ref42","doi-asserted-by":"crossref","first-page":"D1152","DOI":"10.1093\/nar\/gkaa861","article-title":"DockCoV2: a drug database against SARS-CoV-2","volume":"49","author":"Chen","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2024042309553826100_ref43","doi-asserted-by":"crossref","first-page":"D1113","DOI":"10.1093\/nar\/gkaa969","article-title":"COVID19 drug repository: text-mining the literature in search of putative COVID19 therapeutics","volume":"49","author":"Tworowski","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"2024042309553826100_ref44","doi-asserted-by":"crossref","first-page":"D405","DOI":"10.1093\/nar\/gku938","article-title":"The immune epitope database (IEDB) 3.0","volume":"43","author":"Vita","year":"2015","journal-title":"Nucleic Acids Res"},{"issue":"W1","key":"2024042309553826100_ref45","first-page":"W5","article-title":"MAFFT-DASH: integrated protein sequence and structural alignment","volume":"47","author":"Rozewicki","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"21","key":"2024042309553826100_ref46","doi-asserted-by":"crossref","first-page":"2695","DOI":"10.1093\/bioinformatics\/btl461","article-title":"Bio3d: an R package for the comparative analysis of protein structures","volume":"22","author":"Grant","year":"2006","journal-title":"Bioinformatics"},{"key":"2024042309553826100_ref47"},{"issue":"1","key":"2024042309553826100_ref48","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The protein data Bank","volume":"28","author":"Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2024042309553826100_ref49","author":"PyMOL"},{"issue":"W1","key":"2024042309553826100_ref50","doi-asserted-by":"crossref","first-page":"W431","DOI":"10.1093\/nar\/gkab314","article-title":"Mol* viewer: modern web app for 3D visualization and analysis of large biomolecular structures","volume":"49","author":"Sehnal","year":"2021","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"2024042309553826100_ref51","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1093\/bioinformatics\/btz502","article-title":"iCn3D, a web-based 3D viewer for sharing 1D\/2D\/3D representations of biomolecular structures","volume":"36","author":"Wang","year":"2020","journal-title":"Bioinformatics"},{"key":"2024042309553826100_ref52","author":"National Center for Advancing Translational Sciences"},{"issue":"6531","key":"2024042309553826100_ref53","doi-asserted-by":"crossref","first-page":"850","DOI":"10.1126\/science.abf9302","article-title":"Prospective mapping of viral mutations that escape antibodies used to treat COVID-19","volume":"371","author":"Starr","year":"2021","journal-title":"Science"},{"issue":"5","key":"2024042309553826100_ref54","doi-asserted-by":"crossref","first-page":"1295","DOI":"10.1016\/j.cell.2020.08.012","article-title":"Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding","volume":"182","author":"Starr","year":"2020","journal-title":"Cell"},{"issue":"1","key":"2024042309553826100_ref55","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1745-7580-2-2","article-title":"Improved method for predicting linear B-cell epitopes","volume":"2","author":"Larsen","year":"2006","journal-title":"Immunome Res"},{"issue":"W1","key":"2024042309553826100_ref56","doi-asserted-by":"crossref","first-page":"W24","DOI":"10.1093\/nar\/gkx346","article-title":"BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes","volume":"45","author":"Jespersen","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2024042309553826100_ref57","first-page":"45","article-title":"Prediction of the secondary structure of proteins from their amino acid sequence","volume":"47","author":"Chou","year":"1978","journal-title":"Adv Enzymol Relat Areas Mol Biol"},{"issue":"3","key":"2024042309553826100_ref58","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1128\/jvi.55.3.836-839.1985","article-title":"Induction of hepatitis a virus-neutralizing antibody by a virus-specific synthetic peptide","volume":"55","author":"Emini","year":"1985","journal-title":"J Virol"},{"issue":"4","key":"2024042309553826100_ref59","doi-asserted-by":"crossref","first-page":"212","DOI":"10.1007\/BF01195768","article-title":"Prediction of chain flexibility in proteins\u2014a tool for the selection of peptide antigens","volume":"72","author":"Karplus","year":"1985","journal-title":"Naturwissenschaften"},{"issue":"1\u20132","key":"2024042309553826100_ref60","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1016\/0014-5793(90)80535-Q","article-title":"A semi-empirical method for prediction of antigenic determinants on protein antigens","volume":"276","author":"Kolaskar","year":"1990","journal-title":"FEBS Lett"},{"issue":"19","key":"2024042309553826100_ref61","doi-asserted-by":"crossref","first-page":"5425","DOI":"10.1021\/bi00367a013","article-title":"New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites","volume":"25","author":"Parker","year":"1986","journal-title":"Biochemistry"},{"issue":"9","key":"2024042309553826100_ref62","doi-asserted-by":"crossref","first-page":"3360","DOI":"10.4049\/jimmunol.1700893","article-title":"NetMHCpan-4.0: improved peptide-MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data","volume":"199","author":"Jurtz","year":"2017","journal-title":"J Immunol"},{"issue":"1","key":"2024042309553826100_ref63","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1016\/j.cels.2020.06.010","article-title":"MHCflurry 2.0: improved pan-allele prediction of MHC class I-presented peptides by incorporating antigen processing","volume":"11","author":"O\u2019Donnell","year":"2020","journal-title":"Cell Syst"},{"key":"2024042309553826100_ref64","doi-asserted-by":"crossref","first-page":"2559","DOI":"10.3389\/fimmu.2019.02559","article-title":"DeepHLApan: a deep learning approach for Neoantigen prediction considering both HLA-peptide binding and immunogenicity","volume":"10","author":"Wu","year":"2019","journal-title":"Front Immunol"},{"issue":"11","key":"2024042309553826100_ref65","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1038\/s41587-019-0289-6","article-title":"Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes","volume":"37","author":"Racle","year":"2019","journal-title":"Nat Biotechnol"},{"issue":"6","key":"2024042309553826100_ref66","doi-asserted-by":"crossref","first-page":"2304","DOI":"10.1021\/acs.jproteome.9b00874","article-title":"Improved prediction of MHC II antigen presentation through integration and motif deconvolution of mass spectrometry MHC eluted ligand data","volume":"19","author":"Reynisson","year":"2020","journal-title":"J Proteome Res"},{"issue":"7","key":"2024042309553826100_ref67","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0097282","article-title":"HLA diversity in the 1000 genomes dataset","volume":"9","author":"Gourraud","year":"2014","journal-title":"PloS One"},{"issue":"7","key":"2024042309553826100_ref68","doi-asserted-by":"crossref","first-page":"740","DOI":"10.1038\/ng.3576","article-title":"Deep sequencing of the MHC region in the Chinese population contributes to studies of complex disease","volume":"48","author":"Zhou","year":"2016","journal-title":"Nat Genet"},{"key":"2024042309553826100_ref69","author":"Bootstrap"},{"key":"2024042309553826100_ref70","author":"Selectize"},{"key":"2024042309553826100_ref71","author":"DataTables"},{"issue":"2","key":"2024042309553826100_ref72","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1016\/j.visinf.2018.04.011","article-title":"ECharts: a declarative framework for rapid construction of web-based visualization","volume":"2","author":"Li","year":"2018","journal-title":"Vis Inform"},{"key":"2024042309553826100_ref73","article-title":"Interactively visualize genetic mutations using a lollipop-diagram","author":"g3-lollipop.js"},{"issue":"D1","key":"2024042309553826100_ref74","doi-asserted-by":"crossref","first-page":"D506","DOI":"10.1093\/nar\/gky1049","article-title":"UniProt: a worldwide hub of protein knowledge","volume":"47","author":"UniProt Consortium","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"Database issue","key":"2024042309553826100_ref75","doi-asserted-by":"crossref","first-page":"D136","DOI":"10.1093\/nar\/gkr1178","article-title":"The NCBI taxonomy database","volume":"40","author":"Federhen","year":"2012","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"2024042309553826100_ref76","doi-asserted-by":"crossref","first-page":"111845","DOI":"10.1016\/j.celrep.2022.111845","article-title":"Rational identification of potent and broad sarbecovirus-neutralizing antibody cocktails from SARS convalescents","volume":"41","author":"Cao","year":"2022","journal-title":"Cell Rep"},{"issue":"4","key":"2024042309553826100_ref77","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1016\/j.chom.2020.03.002","article-title":"A sequence homology and Bioinformatic approach can predict candidate targets for immune responses to SARS-CoV-2","volume":"27","author":"Grifoni","year":"2020","journal-title":"Cell Host Microbe"},{"key":"2024042309553826100_ref78","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2022.847617","article-title":"Computer-based Immunoinformatic analysis to predict candidate T-cell epitopes for SARS-CoV-2 vaccine design","volume":"13","author":"Mei","year":"2022","journal-title":"Front Immunol"},{"key":"2024042309553826100_ref79","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.addr.2021.01.007","article-title":"In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives","volume":"171","author":"Sohail","year":"2021","journal-title":"Adv Drug Deliv Rev"},{"issue":"3","key":"2024042309553826100_ref80","doi-asserted-by":"crossref","first-page":"bbac070","DOI":"10.1093\/bib\/bbac070","article-title":"A high-throughput single cell-based antibody discovery approach against the full-length SARS-CoV-2 spike protein suggests a lack of neutralizing antibodies targeting the highly conserved S2 domain","volume":"23","author":"Chai","year":"2022","journal-title":"Brief Bioinform"},{"issue":"12","key":"2024042309553826100_ref81","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1038\/s41422-022-00746-3","article-title":"A variant-proof SARS-CoV-2 vaccine targeting HR1 domain in S2 subunit of spike protein","volume":"32","author":"Pang","year":"2022","journal-title":"Cell Res"},{"issue":"3","key":"2024042309553826100_ref82","first-page":"162","article-title":"SARS-CoV-2 variant biology: immune escape, transmission and fitness","volume":"21","author":"Carabelli","year":"2023","journal-title":"Nat Rev Microbiol"},{"issue":"9","key":"2024042309553826100_ref83","doi-asserted-by":"crossref","first-page":"1457","DOI":"10.1038\/s41559-023-02123-8","article-title":"Immune evasion and ACE2 binding affinity contribute to SARS-CoV-2 evolution","volume":"7","author":"Ma","year":"2023","journal-title":"Nat Ecol Evol"},{"issue":"6","key":"2024042309553826100_ref84","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1007\/s43657-022-00066-x","article-title":"Human genetic variants associated with COVID-19 severity are enriched in immune and epithelium regulatory networks","volume":"2","author":"Feng","year":"2022","journal-title":"Phenomics"},{"issue":"4","key":"2024042309553826100_ref85","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1007\/s43657-021-00020-3","article-title":"Molecular phenomic approaches to deconvolving the systemic effects of SARS-CoV-2 infection and post-acute COVID-19 syndrome","volume":"1","author":"Nicholson","year":"2021","journal-title":"Phenomics"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/3\/bbae183\/57299084\/bbae183.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/25\/3\/bbae183\/57299084\/bbae183.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,4,23]],"date-time":"2024-04-23T09:57:01Z","timestamp":1713866221000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbae183\/7655773"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,3,27]]},"references-count":85,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,3,27]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbae183","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,5]]},"published":{"date-parts":[[2024,3,27]]},"article-number":"bbae183"}}