{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T03:30:15Z","timestamp":1768275015124,"version":"3.49.0"},"reference-count":116,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2022,9,1]],"date-time":"2022-09-01T00:00:00Z","timestamp":1661990400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Assessment of protective or harmful T cell response induced by any antigenic epitope is important in designing any immunotherapeutic molecule. The understanding of cytokine induction potential also helps us to monitor antigen-specific cellular immune responses and rational vaccine design. The classical immunoinformatics tools served well for prediction of B cell and T cell epitopes. However, in the last decade, the prediction algorithms for T cell epitope inducing specific cytokines have also been developed and appreciated in the scientific community. This review summarizes the current status of such tools, their applications, background algorithms, their use in experimental setup and functionalities available in the tools\/web servers.<\/jats:p>","DOI":"10.1093\/bib\/bbac382","type":"journal-article","created":{"date-parts":[[2022,9,7]],"date-time":"2022-09-07T21:58:21Z","timestamp":1662587901000},"source":"Crossref","is-referenced-by-count":6,"title":["Not all T cell epitopes are equally desired: a review of<i>in silico<\/i>tools for the prediction of cytokine-inducing potential of T-cell epitopes"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1381-7434","authenticated-orcid":false,"given":"Sandeep Kumar","family":"Dhanda","sequence":"first","affiliation":[{"name":"Department of Oncology, St Jude Children\u2019s Research Hospital , Memphis, Tennessee, USA -38015"},{"name":"Center for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Science , Chennai, India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jitendra","family":"Malviya","sequence":"additional","affiliation":[{"name":"Department of Life Sciences and Biological Science, IES University Bhopal , India"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sudheer","family":"Gupta","sequence":"additional","affiliation":[{"name":"NGS & Bioinformatics Division, 3B BlackBio Biotech India Ltd., 7-C, Industrial Area , Govindpura, Bhopal, India"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,9,6]]},"reference":[{"key":"2022092013240968600_ref1","doi-asserted-by":"crossref","first-page":"278","DOI":"10.3389\/fimmu.2017.00278","article-title":"The immune epitope database and analysis resource in epitope discovery and synthetic vaccine design","volume":"8","author":"Fleri","year":"2017","journal-title":"Front Immunol"},{"issue":"W1","key":"2022092013240968600_ref2","doi-asserted-by":"crossref","first-page":"W502","DOI":"10.1093\/nar\/gkz452","article-title":"IEDB-AR: immune epitope database-analysis resource in 2019","volume":"47","author":"Dhanda","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"2022092013240968600_ref3","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1007757","article-title":"Benchmarking predictions of MHC class I restricted T cell epitopes in a comprehensively studied model system","volume":"16","author":"Paul","year":"2020","journal-title":"PLoS Comput Biol"},{"issue":"5","key":"2022092013240968600_ref4","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1110\/ps.0239403","article-title":"Reliable prediction of T-cell epitopes using neural networks with novel sequence representations","volume":"12","author":"Nielsen","year":"2003","journal-title":"Protein Sci"},{"issue":"199","key":"2022092013240968600_ref5","first-page":"3360","article-title":"NetMHCpan-4.0: improved peptide-MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data","volume":"1950","author":"Jurtz","year":"2017","journal-title":"J Immunol Baltim Md"},{"issue":"5","key":"2022092013240968600_ref6","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1007\/s00251-005-0798-y","article-title":"Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications","volume":"57","author":"Bui","year":"2005","journal-title":"Immunogenetics"},{"issue":"7","key":"2022092013240968600_ref7","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1038\/nbt1215","article-title":"A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus","volume":"24","author":"Moutaftsi","year":"2006","journal-title":"Nat Biotechnol"},{"issue":"4","key":"2022092013240968600_ref8","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1016\/j.cels.2020.09.001","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":"2022092013240968600_ref9","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1093\/bioinformatics\/btg108","article-title":"ProPred1: prediction of promiscuous MHC class-I binding sites","volume":"19","author":"Singh","year":"2003","journal-title":"Bioinforma Oxf Engl"},{"key":"2022092013240968600_ref10","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1007\/s00251-004-0709-7","article-title":"Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles","volume":"56","author":"Reche","year":"2004","journal-title":"Immunogenetics"},{"issue":"1","key":"2022092013240968600_ref11","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1186\/1471-2105-6-132","article-title":"Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method","volume":"6","author":"Peters","year":"2005","journal-title":"BMC Bioinform"},{"key":"2022092013240968600_ref12","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1186\/1471-2105-10-394","article-title":"Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior","volume":"10","author":"Kim","year":"2009","journal-title":"BMC Bioinform"},{"key":"2022092013240968600_ref13","doi-asserted-by":"crossref","first-page":"W254","DOI":"10.1093\/nar\/gkr434","article-title":"PAComplex: a web server to infer peptide antigen families and binding models from TCR-pMHC complexes","volume":"39","author":"Liu","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2022092013240968600_ref14","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1007\/978-1-60327-118-9_5","article-title":"SYFPEITHI: database for searching and T-cell epitope prediction","volume":"409","author":"Schuler","year":"2007","journal-title":"Methods Mol Biol Clifton NJ"},{"issue":"11","key":"2022092013240968600_ref15","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1006457","article-title":"Systematically benchmarking peptide-MHC binding predictors: from synthetic to naturally processed epitopes","volume":"14","author":"Zhao","year":"2018","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"2022092013240968600_ref16","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1111\/imm.12889","article-title":"Improved methods for predicting peptide binding affinity to MHC class II molecules","volume":"154","author":"Jensen","year":"2018","journal-title":"Immunology"},{"issue":"6","key":"2022092013240968600_ref17","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":"4","key":"2022092013240968600_ref18","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000048","article-title":"A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach","volume":"4","author":"Wang","year":"2008","journal-title":"PLoS Comput Biol"},{"key":"2022092013240968600_ref19","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/1471-2105-8-238","article-title":"Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method","volume":"8","author":"Nielsen","year":"2007","journal-title":"BMC Bioinform"},{"issue":"1","key":"2022092013240968600_ref20","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1745-7580-4-2","article-title":"Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries","volume":"4","author":"Sidney","year":"2008","journal-title":"Immunome Res"},{"issue":"2","key":"2022092013240968600_ref21","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0030483","article-title":"TEPITOPEpan: extending TEPITOPE for peptide binding prediction covering over 700 HLA-DR molecules","volume":"7","author":"Zhang","year":"2012","journal-title":"PLoS One"},{"key":"2022092013240968600_ref22","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.3389\/fimmu.2018.01369","article-title":"Predicting HLA CD4 immunogenicity in human populations","volume":"9","author":"Dhanda","year":"2018","journal-title":"Front Immunol"},{"issue":"10","key":"2022092013240968600_ref23","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003266","article-title":"Properties of MHC class I presented peptides that enhance immunogenicity","volume":"9","author":"Calis","year":"2013","journal-title":"PLoS Comput Biol"},{"key":"2022092013240968600_ref24","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1002\/cyto.a.10023","article-title":"Comparison of proliferation and rapid cytokine induction assays for flow cytometric T-cell epitope mapping","volume":"52","author":"Tesfa","year":"2003","journal-title":"Cytom Part J Int Soc Anal Cytol"},{"issue":"sup1","key":"2022092013240968600_ref25","doi-asserted-by":"crossref","first-page":"197","DOI":"10.3109\/02713689208999533","article-title":"Cytokine induction by immunomodulatory epitopes in S-antigen and tumor necrosis factor alpha","volume":"11","author":"Stiemer","year":"1992","journal-title":"Curr Eye Res"},{"issue":"3","key":"2022092013240968600_ref26","first-page":"467","article-title":"Novel in silico tools for designing peptide-based subunit vaccines and immunotherapeutics","volume":"18","author":"Dhanda","year":"2017","journal-title":"Brief Bioinform"},{"issue":"D1","key":"2022092013240968600_ref27","doi-asserted-by":"crossref","first-page":"D339","DOI":"10.1093\/nar\/gky1006","article-title":"The Immune Epitope Database (IEDB): 2018 update","volume":"47","author":"Vita","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"2022092013240968600_ref28","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0153771","article-title":"A web-based platform for designing vaccines against existing and emerging strains of Mycobacterium tuberculosis","volume":"11","author":"Dhanda","year":"2016","journal-title":"PLoS One"},{"key":"2022092013240968600_ref29","first-page":"163","article-title":"Two faces of milk proteins peptides with both allergenic and multidimensional health beneficial impact- integrated in vitro\/in silico approach","volume":"10","author":"Ogrodowczyk","year":"2021","journal-title":"Foods Basel Switz"},{"key":"2022092013240968600_ref30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/07391102.2021.1953599","article-title":"Childhood type 1 diabetes mellitus and risk factor of interactions between dietary cow\u2019s milk intake and HLA-DR3\/DR4 genotype","author":"Benslama","year":"2021","journal-title":"J Biomol Struct Dyn"},{"key":"2022092013240968600_ref31","doi-asserted-by":"crossref","first-page":"1938","DOI":"10.3389\/fmicb.2017.01938","article-title":"Morbid sequences suggest molecular mimicry between microbial peptides and self-antigens: a possibility of inciting autoimmunity","volume":"8","author":"Pahari","year":"2017","journal-title":"Front Microbiol"},{"key":"2022092013240968600_ref32","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1111\/fcp.12690","article-title":"Combination of human papillomaviruses L1 and L2 multiepitope constructs protects mice against tumor cells","volume":"35","author":"Namvar","year":"2021","journal-title":"Fundam Clin Pharmacol"},{"key":"2022092013240968600_ref33","doi-asserted-by":"crossref","DOI":"10.1016\/j.intimp.2020.107265","article-title":"Immuno-informatics analysis and expression of a novel multi-domain antigen as a vaccine candidate against glioblastoma","volume":"91","author":"Gharbavi","year":"2021","journal-title":"Int Immunopharmacol"},{"key":"2022092013240968600_ref34","doi-asserted-by":"crossref","first-page":"1763","DOI":"10.3389\/fimmu.2017.01763","article-title":"Identification of potential MHC class-II-restricted epitopes derived from Leishmania donovani antigens by reverse vaccinology and evaluation of their CD4+ T-cell responsiveness against visceral leishmaniasis","volume":"8","author":"Dikhit","year":"2017","journal-title":"Front Immunol"},{"key":"2022092013240968600_ref35","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1186\/1745-6150-8-30","article-title":"Designing of interferon-gamma inducing MHC class-II binders","volume":"8","author":"Dhanda","year":"2013","journal-title":"Biol Direct"},{"key":"2022092013240968600_ref36","doi-asserted-by":"crossref","DOI":"10.1155\/2013\/263952","article-title":"Prediction of IL4 inducing peptides","volume":"2013","author":"Dhanda","year":"2013","journal-title":"Clin Dev Immunol"},{"issue":"1","key":"2022092013240968600_ref37","doi-asserted-by":"crossref","first-page":"42851","DOI":"10.1038\/srep42851","article-title":"Computer-aided designing of immunosuppressive peptides based on IL-10 inducing potential","volume":"7","author":"Nagpal","year":"2017","journal-title":"Sci Rep"},{"key":"2022092013240968600_ref38","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1093\/bib\/bbaa259","article-title":"Computer-aided prediction and design of IL-6 inducing peptides: IL-6 plays a crucial role in COVID-19","volume":"22","author":"Dhall","year":"2021","journal-title":"Brief Bioinform"},{"issue":"6","key":"2022092013240968600_ref39","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbab172","article-title":"StackIL6: a stacking ensemble model for improving the prediction of IL-6 inducing peptides","volume":"22","author":"Charoenkwan","year":"2021","journal-title":"Brief Bioinform"},{"key":"2022092013240968600_ref40","doi-asserted-by":"crossref","first-page":"1430","DOI":"10.3389\/fimmu.2017.01430","article-title":"IL17eScan: a tool for the identification of peptides inducing IL-17 response","volume":"8","author":"Gupta","year":"2017","journal-title":"Front Immunol"},{"key":"2022092013240968600_ref41","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.molimm.2020.02.009","article-title":"Structural basis and designing of peptide vaccine using PE-PGRS family protein of Mycobacterium ulcerans-an integrated vaccinomics approach","volume":"120","author":"Nain","year":"2020","journal-title":"Mol Immunol"},{"issue":"1","key":"2022092013240968600_ref42","doi-asserted-by":"crossref","first-page":"15431","DOI":"10.1038\/s41598-021-92176-1","article-title":"Designing a multi-epitope vaccine candidate to combat MERS-CoV by employing an immunoinformatics approach","volume":"11","author":"Mahmud","year":"2021","journal-title":"Sci Rep"},{"key":"2022092013240968600_ref43","doi-asserted-by":"crossref","first-page":"6585","DOI":"10.1080\/07391102.2020.1803969","article-title":"Designing novel epitope-based polyvalent vaccines against herpes simplex virus-1 and 2 exploiting the immunoinformatics approach","volume":"39","author":"Sarkar","year":"2020","journal-title":"J Biomol Struct Dyn"},{"key":"2022092013240968600_ref44","doi-asserted-by":"crossref","DOI":"10.1016\/j.imu.2020.100478","article-title":"Engineering a novel subunit vaccine against SARS-CoV-2 by exploring immunoinformatics approach","volume":"21","author":"Sarkar","year":"2020","journal-title":"Inform Med Unlocked"},{"key":"2022092013240968600_ref45","doi-asserted-by":"crossref","first-page":"787","DOI":"10.3390\/v13050787","article-title":"Identification of highly conserved SARS-CoV-2 antigenic epitopes with wide coverage using reverse vaccinology approach","volume":"13","author":"Hisham","year":"2021","journal-title":"Viruses"},{"key":"2022092013240968600_ref46","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0240577","article-title":"Design of novel multiepitope constructs-based peptide vaccine against the structural S, N and M proteins of human COVID-19 using immunoinformatics analysis","volume":"15","author":"Khairkhah","year":"2020","journal-title":"PLoS One"},{"key":"2022092013240968600_ref47","doi-asserted-by":"crossref","first-page":"3","DOI":"10.3390\/pathogens10010003","article-title":"The tip region on VP2 protein of bluetongue virus contains potential IL-4-inducing amino acid peptide segments","volume":"10","author":"Yang","year":"2020","journal-title":"Pathog Basel Switz"},{"key":"2022092013240968600_ref48","doi-asserted-by":"crossref","DOI":"10.1016\/j.imu.2021.100678","article-title":"Immunoinformatics aided-design of novel multi-epitope based peptide vaccine against Hendra henipavirus through proteome exploration","volume":"25","author":"Hossan","year":"2021","journal-title":"Inform Med Unlocked"},{"issue":"8","key":"2022092013240968600_ref49","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1007\/s10529-021-03143-9","article-title":"In silico design and in vitro expression of novel multiepitope DNA constructs based on HIV-1 proteins and Hsp70 T-cell epitopes","volume":"43","author":"Akbari","year":"2021","journal-title":"Biotechnol Lett"},{"key":"2022092013240968600_ref50","article-title":"Rational design of multimeric based subunit vaccine against Mycoplasma pneumonia: subtractive proteomics with immunoinformatics framework","volume":"91","author":"Mahmood","year":"2021","journal-title":"Infect Genet Evol J Mol Epidemiol Evol Genet Infect Dis"},{"issue":"20","key":"2022092013240968600_ref51","doi-asserted-by":"crossref","first-page":"3671","DOI":"10.1016\/j.vaccine.2020.03.023","article-title":"Development of a multivalent enterovirus subunit vaccine based on immunoinformatic design principles for the prevention of HFMD","volume":"38","author":"Deng","year":"2020","journal-title":"Vaccine"},{"key":"2022092013240968600_ref52","article-title":"Discovery of potential immune epitopes and peptide vaccine design - a prophylactic strategy against Rift Valley fever virus","volume":"9","author":"Nain","journal-title":"F1000Research"},{"issue":"16","key":"2022092013240968600_ref53","doi-asserted-by":"crossref","first-page":"4850","DOI":"10.1080\/07391102.2019.1692072","article-title":"Proteome-wide screening for designing a multi-epitope vaccine against emerging pathogen Elizabethkingia anophelis using immunoinformatic approaches","volume":"38","author":"Nain","year":"2020","journal-title":"J Biomol Struct Dyn"},{"issue":"7","key":"2022092013240968600_ref54","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1016\/j.vaccine.2021.01.003","article-title":"Immunoinformatics prediction of overlapping CD8+ T-cell, IFN-\u03b3 and IL-4 inducer CD4+ T-cell and linear B-cell epitopes based vaccines against COVID-19 (SARS-CoV-2)","volume":"39","author":"Fatoba","year":"2021","journal-title":"Vaccine"},{"key":"2022092013240968600_ref55","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/j.molimm.2017.11.024","article-title":"In silico prediction of potential vaccine candidates on capsid protein of human bocavirus 1","volume":"93","author":"Kalyanaraman","year":"2018","journal-title":"Mol Immunol"},{"key":"2022092013240968600_ref56","doi-asserted-by":"crossref","DOI":"10.1016\/j.micpath.2021.104996","article-title":"Mining the Mycobacterium tuberculosis proteome for identification of potential T-cell epitope based vaccine candidates","volume":"157","author":"Madan","year":"2021","journal-title":"Microb Pathog"},{"key":"2022092013240968600_ref57","first-page":"107","article-title":"Prediction and analysis of promiscuous T cell-epitopes derived from the vaccine candidate antigens of Leishmania donovani binding to MHC class-II alleles using in silico approach","volume":"53","author":"Kashyap","year":"2017","journal-title":"Infect Genet Evol J Mol Epidemiol Evol Genet Infect Dis"},{"key":"2022092013240968600_ref58","doi-asserted-by":"crossref","first-page":"4555","DOI":"10.1016\/j.vaccine.2018.05.082","article-title":"Development of multi-epitope driven subunit vaccine in secretory and membrane protein of Plasmodium falciparum to convey protection against malaria infection","volume":"36","author":"Pandey","year":"2018","journal-title":"Vaccine"},{"issue":"4","key":"2022092013240968600_ref59","doi-asserted-by":"crossref","first-page":"2089","DOI":"10.1007\/s10989-019-10003-8","article-title":"Exploring lassa virus proteome to design a multi-epitope vaccine through immunoinformatics and immune simulation analyses","volume":"26","author":"Sayed","year":"2020","journal-title":"Int J Pept Res Ther"},{"key":"2022092013240968600_ref60","article-title":"Towards the development of a novel vaccine for Trichuris trichiura | Research Explorer | The University of Manchester","author":"Zawawi"},{"key":"2022092013240968600_ref61","doi-asserted-by":"crossref","DOI":"10.20944\/preprints202105.0400.v1","article-title":"Designing a multi-epitope vaccine against dracunculus medinensis by employing immuno-informatics and in silico approaches","volume-title":"Preprints","author":"Sarfraz","year":"2021"},{"key":"2022092013240968600_ref62","doi-asserted-by":"crossref","DOI":"10.1016\/j.micpath.2020.104705","article-title":"A comprehensive screening of the whole proteome of hantavirus and designing a multi-epitope subunit vaccine for cross-protection against hantavirus: structural vaccinology and immunoinformatics study","volume":"150","author":"Abdulla","year":"2021","journal-title":"Microb Pathog"},{"key":"2022092013240968600_ref63","doi-asserted-by":"crossref","first-page":"20864","DOI":"10.1038\/s41598-020-77547-4","article-title":"Immunoinformatic design of a COVID-19 subunit vaccine using entire structural immunogenic epitopes of SARS-CoV-2","volume":"10","author":"Behmard","year":"2020","journal-title":"Sci Rep"},{"key":"2022092013240968600_ref64","article-title":"Immunoinformatic construction of an adenovirus-based modular vaccine platform and its application in the design of a SARS-CoV-2 vaccine","volume":"85","author":"Porto","year":"2020","journal-title":"Infect Genet Evol J Mol Epidemiol Evol Genet Infect Dis"},{"key":"2022092013240968600_ref65","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1080\/07391102.2020.1792347","article-title":"Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach","volume":"40","author":"Samad","year":"2020","journal-title":"J Biomol Struct Dyn"},{"key":"2022092013240968600_ref66","doi-asserted-by":"crossref","first-page":"820","DOI":"10.1016\/j.ijbiomac.2020.06.213","article-title":"Designing a novel mRNA vaccine against SARS-CoV-2: an immunoinformatics approach","volume":"162","author":"Ahammad","year":"2020","journal-title":"Int J Biol Macromol"},{"issue":"29","key":"2022092013240968600_ref67","doi-asserted-by":"crossref","first-page":"18103","DOI":"10.1039\/D1RA02885E","article-title":"Immunoinformatics-guided design of a multi-epitope vaccine based on the structural proteins of severe acute respiratory syndrome coronavirus 2","volume":"11","author":"Obaidullah","year":"2021","journal-title":"RSC Adv"},{"issue":"12","key":"2022092013240968600_ref68","doi-asserted-by":"crossref","first-page":"1192","DOI":"10.1007\/s12033-021-00374-z","article-title":"In silico design and immunological studies of two novel multiepitope DNA-based vaccine candidates against high-risk human papillomaviruses","volume":"63","author":"Kayyal","year":"2021","journal-title":"Mol Biotechnol"},{"key":"2022092013240968600_ref69","doi-asserted-by":"crossref","first-page":"468","DOI":"10.1186\/s12859-018-2482-x","article-title":"Exploitation of reverse vaccinology and immunoinformatics as promising platform for genome-wide screening of new effective vaccine candidates against Plasmodium falciparum","volume":"19","author":"Pritam","year":"2019","journal-title":"BMC Bioinform"},{"key":"2022092013240968600_ref70","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/s43141-021-00199-y","article-title":"Screening and characterization of hypothetical proteins of Plasmodium falciparum as novel vaccine candidates in the fight against malaria using reverse vaccinology","volume":"19","author":"Aguttu","year":"2021","journal-title":"J Genet Eng Biotechnol"},{"key":"2022092013240968600_ref71","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/14760584.2021.1874925","article-title":"Immunoinformatics-guided designing and in silico analysis of epitope-based polyvalent vaccines against multiple strains of human coronavirus (HCoV)","author":"Sarkar","year":"2021","journal-title":"Expert Rev Vaccines"},{"key":"2022092013240968600_ref72","first-page":"1","article-title":"Immunoinformatics analysis to design novel epitope based vaccine candidate targeting the glycoprotein and nucleoprotein of Lassa mammarenavirus (LASMV) using strains from Nigeria","volume":"1\u201320","author":"Abass","year":"2021","journal-title":"J Biomol Struct Dyn"},{"issue":"6","key":"2022092013240968600_ref73","doi-asserted-by":"crossref","first-page":"658","DOI":"10.3390\/vaccines9060658","article-title":"Integrated core proteomics, subtractive proteomics, and immunoinformatics investigation to unveil a potential multi-epitope vaccine against Schistosomiasis","volume":"9","author":"Rehman","year":"2021","journal-title":"Vaccine"},{"key":"2022092013240968600_ref74","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/10495398.2021.1899937","article-title":"Computational design of a new multi-epitope vaccine using immunoinformatics approach against mastitis disease","volume":"1\u201312","author":"Dzayee","year":"2021","journal-title":"Anim Biotechnol"},{"key":"2022092013240968600_ref75","doi-asserted-by":"crossref","DOI":"10.1016\/j.imu.2020.100500","article-title":"Immunoinformatics approach to designing a multi-epitope vaccine against Saint Louis Encephalitis Virus","volume":"22","author":"Hossain","year":"2021","journal-title":"Inform Med Unlocked"},{"issue":"1","key":"2022092013240968600_ref76","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1186\/s13071-020-04064-8","article-title":"An immunoinformatic approach driven by experimental proteomics: in silico design of a subunit candidate vaccine targeting secretory proteins of Leishmania donovani amastigotes","volume":"13","author":"Khan","year":"2020","journal-title":"Parasit Vectors"},{"key":"2022092013240968600_ref77","doi-asserted-by":"crossref","first-page":"6882","DOI":"10.1080\/07391102.2020.1804456","article-title":"Blueprint of epitope-based multivalent and multipathogenic vaccines: targeted against the dengue and zika viruses","volume":"39","author":"Sarkar","year":"2020","journal-title":"J Biomol Struct Dyn"},{"issue":"3","key":"2022092013240968600_ref78","doi-asserted-by":"crossref","DOI":"10.1016\/j.heliyon.2021.e06396","article-title":"Implementation of in silico methods to predict common epitopes for vaccine development against Chikungunya and Mayaro viruses","volume":"7","author":"Hoque","year":"2021","journal-title":"Heliyon"},{"key":"2022092013240968600_ref79","doi-asserted-by":"crossref","DOI":"10.1016\/j.mcp.2020.101693","article-title":"Computational formulation and immune dynamics of a multi-peptide vaccine candidate against Crimean-Congo hemorrhagic fever virus","volume":"55","author":"Khan","year":"2021","journal-title":"Mol Cell Probes"},{"key":"2022092013240968600_ref80","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2021.666223","article-title":"Profile of circulatory cytokines and chemokines in human coronaviruses: a systematic review and meta-analysis","volume":"12","author":"Zawawi","year":"2021","journal-title":"Front Immunol"},{"issue":"10","key":"2022092013240968600_ref81","doi-asserted-by":"crossref","first-page":"930","DOI":"10.1016\/j.biopsych.2010.06.012","article-title":"A meta-analysis of cytokines in Alzheimer\u2019s disease","volume":"68","author":"Swardfager","year":"2010","journal-title":"Biol Psychiatry"},{"issue":"1","key":"2022092013240968600_ref82","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1186\/s12974-017-0961-z","article-title":"Increased frequency of IL-6-producing non-classical monocytes in neuromyelitis optica spectrum disorder","volume":"14","author":"Kong","year":"2017","journal-title":"J Neuroinflammation"},{"issue":"5","key":"2022092013240968600_ref83","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1191\/0961203304lu1023oa","article-title":"Rationale for interleukin-6 blockade in systemic lupus erythematosus","volume":"13","author":"Tackey","year":"2004","journal-title":"Lupus"},{"key":"2022092013240968600_ref84","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1007\/s40203-021-00098-7","article-title":"Prediction and identification of T cell epitopes of COVID-19 with balanced cytokine response for the development of peptide based vaccines","volume":"9","author":"","year":"2021","journal-title":"Silico Pharmacol"},{"issue":"6","key":"2022092013240968600_ref85","doi-asserted-by":"crossref","DOI":"10.1093\/bib\/bbab226","article-title":"DeepR2cov: deep representation learning on heterogeneous drug networks to discover anti-inflammatory agents for COVID-19","volume":"22","author":"Wang","year":"2021","journal-title":"Brief Bioinform"},{"issue":"1","key":"2022092013240968600_ref86","doi-asserted-by":"crossref","first-page":"54","DOI":"10.3390\/vaccines9010054","article-title":"Nucleocapsid and spike proteins of the coronavirus SARS-CoV-2 induce IL6 in monocytes and macrophages-potential implications for Cytokine Storm syndrome","volume":"9","author":"Karwaciak","year":"2021","journal-title":"Vaccine"},{"issue":"6","key":"2022092013240968600_ref87","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1111\/omi.12038","article-title":"Identification of gingipain-specific I-A(b) -restricted CD4+ T cells following mucosal colonization with Porphyromonas gingivalis in C57BL\/6 mice","volume":"28","author":"Bittner-Eddy","year":"2013","journal-title":"Mol Oral Microbiol"},{"key":"2022092013240968600_ref88","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1007\/s11926-009-0052-y","article-title":"The role of interleukin-17 in the pathogenesis of rheumatoid arthritis","volume":"11","author":"Gaffen","year":"2009","journal-title":"Curr Rheumatol Rep"},{"issue":"4","key":"2022092013240968600_ref89","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1080\/030097402320318387","article-title":"Cytokine profile in Beh\u00e7et\u2019s disease patients. Relationship with disease activity","volume":"31","author":"Hamzaoui","year":"2002","journal-title":"Scand J Rheumatol"},{"issue":"2","key":"2022092013240968600_ref90","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1084\/jem.20041257","article-title":"IL-23 drives a pathogenic T cell population that induces autoimmune inflammation","volume":"201","author":"Langrish","year":"2005","journal-title":"J Exp Med"},{"key":"2022092013240968600_ref91","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1191\/096120300678828703","article-title":"Elevation of proinflammatory cytokine (IL-18, IL-17, IL-12) and Th2 cytokine (IL-4) concentrations in patients with systemic lupus erythematosus","volume":"9","author":"Wong","year":"2000","journal-title":"Lupus"},{"issue":"11","key":"2022092013240968600_ref92","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.1038\/ni1261","article-title":"A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17","volume":"6","author":"Park","year":"2005","journal-title":"Nat Immunol"},{"key":"2022092013240968600_ref93","doi-asserted-by":"crossref","DOI":"10.1016\/j.imu.2021.100673","article-title":"Functional engineering of OprF-OprI-PopB as a chimeric immunogen and its cross-protective evaluation with GM-CSF against Pseudomonas aeruginosa: a comprehensive immunoinformatics evaluation","volume":"25","author":"Sabzehali","year":"2021","journal-title":"Inform Med Unlocked"},{"key":"2022092013240968600_ref94","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1186\/s12967-016-0928-3","article-title":"ProInflam: a webserver for the prediction of proinflammatory antigenicity of peptides and proteins","volume":"14","author":"Gupta","year":"2016","journal-title":"J Transl Med"},{"key":"2022092013240968600_ref95","doi-asserted-by":"crossref","first-page":"1783","DOI":"10.3389\/fimmu.2018.01783","article-title":"PIP-EL: a new ensemble learning method for improved proinflammatory peptide predictions","volume":"9","author":"Manavalan","year":"2018","journal-title":"Front Immunol"},{"key":"2022092013240968600_ref96","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1007\/s10822-020-00343-9","article-title":"ProIn-Fuse: improved and robust prediction of proinflammatory peptides by fusing of multiple feature representations","volume":"34","author":"Khatun","year":"2020","journal-title":"J Comput Aided Mol Des"},{"issue":"6","key":"2022092013240968600_ref97","doi-asserted-by":"crossref","first-page":"1700","DOI":"10.1128\/AAC.45.6.1700-1704.2001","article-title":"Proinflammatory activity of a cecropin-like antibacterial peptide from Helicobacter pylori","volume":"45","author":"Bylund","year":"2001","journal-title":"Antimicrob Agents Chemother"},{"issue":"174","key":"2022092013240968600_ref98","first-page":"2235","article-title":"A proinflammatory peptide from herpes simplex virus type 2 glycoprotein G affects neutrophil, monocyte, and NK cell functions","volume":"1950","author":"Bellner","year":"2005","journal-title":"J Immunol Baltim Md"},{"key":"2022092013240968600_ref99","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1189\/jlb.1102521","article-title":"Activation by prion peptide PrP106-126 induces a NF-kappaB-driven proinflammatory response in human monocyte-derived dendritic cells","volume":"74","author":"Bacot","year":"2003","journal-title":"J Leukoc Biol"},{"issue":"10","key":"2022092013240968600_ref100","first-page":"4895","article-title":"Little peptide, big effects: the role of LL-37 in inflammation and autoimmune disease","volume":"191","author":"Kahlenberg","year":"2013","journal-title":"J Immunol Baltim Md"},{"issue":"5","key":"2022092013240968600_ref101","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0195023","article-title":"Bacteriophage cocktail for biocontrol of Escherichia coli O157:H7: Stability and potential allergenicity study","volume":"13","author":"Ramirez","year":"2018","journal-title":"PLoS One"},{"key":"2022092013240968600_ref102","doi-asserted-by":"crossref","first-page":"129","DOI":"10.3389\/fgene.2019.00129","article-title":"PreAIP: computational prediction of anti-inflammatory peptides by integrating multiple complementary features","volume":"10","author":"Khatun","year":"2019","journal-title":"Front Genet"},{"key":"2022092013240968600_ref103","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s12967-016-1103-6","article-title":"Prediction of anti-inflammatory proteins\/peptides: an insilico approach","volume":"15","author":"Gupta","year":"2017","journal-title":"J Transl Med"},{"key":"2022092013240968600_ref104","doi-asserted-by":"crossref","first-page":"276","DOI":"10.3389\/fphar.2018.00276","article-title":"AIPpred: sequence-based prediction of anti-inflammatory peptides using random forest","volume":"9","author":"Manavalan","year":"2018","journal-title":"Front Pharmacol"},{"key":"2022092013240968600_ref105","article-title":"AIEpred: an ensemble predictive model of classifier chain to identify anti-inflammatory peptides","volume":"18","author":"Zhang","year":"2020","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"},{"issue":"4","key":"2022092013240968600_ref106","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1002\/1531-8249(200010)48:4<567::AID-ANA3>3.0.CO;2-W","article-title":"Nasal administration of amyloid-beta peptide decreases cerebral amyloid burden in a mouse model of Alzheimer\u2019s disease","volume":"48","author":"Weiner","year":"2000","journal-title":"Ann Neurol"},{"key":"2022092013240968600_ref107","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/87887","article-title":"Vasoactive intestinal peptide prevents experimental arthritis by downregulating both autoimmune and inflammatory components of the disease","volume":"7","author":"Delgado","year":"2001","journal-title":"Nat Med"},{"issue":"5","key":"2022092013240968600_ref108","doi-asserted-by":"crossref","first-page":"1516","DOI":"10.1111\/j.1471-4159.2009.06076.x","article-title":"A synthetic NCAM-derived mimetic peptide, FGL, exerts anti-inflammatory properties via IGF-1 and interferon-gamma modulation","volume":"109","author":"Downer","year":"2009","journal-title":"J Neurochem"},{"issue":"7\u20138","key":"2022092013240968600_ref109","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1080\/14789450.2020.1829486","article-title":"Taenia solium proteins: a beautiful kaleidoscope of pro and anti-inflammatory antigens","volume":"17","author":"Arora","year":"2020","journal-title":"Expert Rev Proteomics"},{"issue":"9","key":"2022092013240968600_ref110","doi-asserted-by":"crossref","first-page":"1147","DOI":"10.3390\/foods9091147","article-title":"An artificial intelligence characterised functional ingredient, derived from rice, inhibits TNF-\u03b1 and significantly improves physical strength in an inflammaging population","volume":"9","author":"Kennedy","year":"2020","journal-title":"Foods"},{"issue":"Web Server","key":"2022092013240968600_ref111","doi-asserted-by":"crossref","first-page":"W202","DOI":"10.1093\/nar\/gkp335","article-title":"MEME SUITE: tools for motif discovery and searching","volume":"37","author":"Bailey","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2022092013240968600_ref112","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1093\/bioinformatics\/btr110","article-title":"Identifying discriminative classification-based motifs in biological sequences","volume":"27","author":"Vens","year":"2011","journal-title":"Bioinforma Oxf Engl"},{"key":"2022092013240968600_ref113","doi-asserted-by":"crossref","first-page":"1873","DOI":"10.1517\/14712590802494501","article-title":"The good, the bad and the ugly: how altered peptide ligands modulate immunity","volume":"8","author":"Katsara","year":"2008","journal-title":"Expert Opin Biol Ther"},{"key":"2022092013240968600_ref114","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/0952-7915(95)80035-2","article-title":"Significance of T-cell stimulation by altered peptide ligands in T cell biology","volume":"7","author":"Sloan-Lancaster","year":"1995","journal-title":"Curr Opin Immunol"},{"issue":"4","key":"2022092013240968600_ref115","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1016\/j.ymthe.2018.01.015","article-title":"Altered peptide ligands impact the diversity of polyfunctional phenotypes in T cell receptor gene-modified T cells","volume":"26","author":"Spear","year":"2018","journal-title":"Mol Ther"},{"issue":"1","key":"2022092013240968600_ref116","doi-asserted-by":"crossref","first-page":"bbab403","DOI":"10.1093\/bib\/bbab403","article-title":"A multi-step and multi-scale bioinformatic protocol to investigate potential SARS-CoV-2 vaccine targets","volume":"23","author":"Russo","year":"2022","journal-title":"Brief Bioinform"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/5\/bbac382\/45939744\/bbac382.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/23\/5\/bbac382\/45939744\/bbac382.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,26]],"date-time":"2023-11-26T04:30:25Z","timestamp":1700973025000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbac382\/6692551"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,9]]},"references-count":116,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2022,9,20]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbac382","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,9]]},"published":{"date-parts":[[2022,9]]},"article-number":"bbac382"}}