{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T06:57:45Z","timestamp":1785567465701,"version":"3.56.0"},"reference-count":208,"publisher":"Springer Science and Business Media LLC","license":[{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T00:00:00Z","timestamp":1785542400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Folia Microbiol"],"DOI":"10.1007\/s12223-026-01565-4","type":"journal-article","created":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T04:56:13Z","timestamp":1785560173000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Immunoinformatics-driven multi-epitope vaccine design as a promising strategy against multidrug-resistant pathogens: a comprehensive review"],"prefix":"10.1007","author":[{"given":"Rameen","family":"Nasir","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Mutayyab","family":"Javaid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raheen","family":"Rahman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rimsha","family":"Abbasi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muneeb","family":"Khalid","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad","family":"Arslan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Amjad","family":"Sajjad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1794-8642","authenticated-orcid":false,"given":"Ahsan","family":"Ibrahim","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,8,1]]},"reference":[{"issue":"4","key":"1565_CR1","first-page":"37","volume":"4","author":"S Ahmad","year":"2021","unstructured":"Ahmad S, Singh S, Srivastava MR, Shukla S, Rai S, Shamsi AS (2021) Molecular docking simplified: literature review. Adv Med Dent Health Sci 4(4):37\u201344","journal-title":"Adv Med Dent Health Sci"},{"key":"1565_CR2","doi-asserted-by":"publisher","DOI":"10.1016\/j.glmedi.2024.100081","volume":"2","author":"SK Ahmed","year":"2024","unstructured":"Ahmed SK, Hussein S, Qurbani K, Ibrahim RH, Fareeq A, Mahmood KA, Mohamed MG (2024) Antimicrobial resistance: impacts, challenges, and future prospects. J Med Surg Public Health 2:100081. https:\/\/doi.org\/10.1016\/j.glmedi.2024.100081","journal-title":"J Med Surg Public Health"},{"issue":"1","key":"1565_CR3","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-025-11768-3","volume":"15","author":"E Akurut","year":"2025","unstructured":"Akurut E, Gavamukulya Y, Mulindwa J, Isiagi M, Galiwango R, Bbuye M, Lujumba I, Kiberu D, Nabisubi P, Kebirungi G, Kambugu A, Castelnuovo B, Nkurunungi G, Jjingo D, Oketch B, Kateete DP, Mboowa G (2025) Design of a multi-epitope vaccine against drug-resistant Mycobacterium tuberculosis and Mycobacterium bovis using reverse vaccinology. Sci Rep 15(1):27298. https:\/\/doi.org\/10.1038\/s41598-025-11768-3","journal-title":"Sci Rep"},{"key":"1565_CR4","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2024.1454394","volume":"15","author":"HH Alhassan","year":"2024","unstructured":"Alhassan HH (2024a) Advanced vaccinomic, immunoinformatic, and molecular modeling strategies for designing multi-epitope vaccines against the Enterobacter cloacae complex. Front Immunol 15:1454394. https:\/\/doi.org\/10.3389\/fimmu.2024.1454394","journal-title":"Front Immunol"},{"key":"1565_CR5","doi-asserted-by":"crossref","unstructured":"Alhassan HH (2024b) \u201cAdvanced vaccinomic, immunoinformatic, and molecular modeling strategies for designing Multi-epitope vaccines against the Enterobacter cloacae complex.\u201d Frontiers in Immunology 15:1454394.","DOI":"10.3389\/fimmu.2024.1454394"},{"issue":"1","key":"1565_CR6","doi-asserted-by":"publisher","first-page":"31745","DOI":"10.1038\/s41598-025-01201-0","volume":"15","author":"A Ali","year":"2025","unstructured":"Ali A, Hamid MHB, Nasir S, Ishaq Z, Anwer F (2025) B-vac a robust software package for bacterial vaccine design. Sci Rep 15(1):31745","journal-title":"Sci Rep"},{"key":"1565_CR7","doi-asserted-by":"publisher","first-page":"1546254","DOI":"10.3389\/fimmu.2025.1546254","volume":"16","author":"H Alnajran","year":"2025","unstructured":"Alnajran H, Awadalla M, Aldakheel FM, Alam I, Momin AA, Alturaiki W, Alosaimi B (2025) Design of a peptide-based vaccine against human respiratory syncytial virus using a reverse vaccinology approach: evaluation of immunogenicity, antigenicity, allergenicity, and toxicity. Front Immunol 16:1546254","journal-title":"Front Immunol"},{"issue":"2","key":"1565_CR8","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1021\/acs.jcim.6b00443","volume":"57","author":"H Alogheli","year":"2017","unstructured":"Alogheli H, Olanders G, Schaal W, Brandt P, Karl\u00e9n A (2017) Docking of macrocycles: comparing rigid and flexible docking in Glide. J Chem Inf Model 57(2):190\u2013202","journal-title":"J Chem Inf Model"},{"issue":"11","key":"1565_CR9","doi-asserted-by":"publisher","first-page":"e1007719","DOI":"10.1371\/journal.pcbi.1007719","volume":"16","author":"SD Anderson","year":"2020","unstructured":"Anderson SD, Tabassum A, Yeon JK, Sharma G, Santos P, Soong TH, Win Thu Y, Nies I, Kurita T, Chandler A, Alsamarah A, Kanassatega RS, Luo Y, Botello-Smith WM, Andresen BT (2020) In silico prediction of ARB resistance: A first step in creating personalized ARB therapy. PLoS Comput Biol 16(11):e1007719","journal-title":"PLoS Comput Biol"},{"key":"1565_CR10","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1016\/B978-0-443-18564-9.00030-8","volume-title":"Advanced Vaccination Technologies for Infectious and Chronic Diseases","author":"T Andey","year":"2024","unstructured":"Andey T, Soni S, Modi S (2024) Conventional vaccination methods: Inactivated and live attenuated vaccines. Advanced Vaccination Technologies for Infectious and Chronic Diseases. pp 37\u201350"},{"key":"1565_CR11","doi-asserted-by":"crossref","unstructured":"Apost\u00f3lico JS, Lunardelli VAS, Coirada FC, Boscardin SB, Rosa DS (2016) Adjuvants: classification, modus operandi, and licensing. J Immunol Res 2016:1459394","DOI":"10.1155\/2016\/1459394"},{"key":"1565_CR12","doi-asserted-by":"publisher","first-page":"1459394","DOI":"10.1155\/2016\/1459394","volume":"2016","author":"JS Apost\u00f3lico","year":"2016","unstructured":"Apost\u00f3lico JS, Lunardelli VAS, Coirada FC, Boscardin SB, Rosa DS (2016) Adjuvants: classification, modus operandi, and licensing. J Immunol Res 2016:1459394. https:\/\/doi.org\/10.1155\/2016\/1459394","journal-title":"J Immunol Res"},{"issue":"1","key":"1565_CR13","doi-asserted-by":"publisher","first-page":"22610","DOI":"10.1038\/s41598-025-07433-4","volume":"15","author":"C Aram","year":"2025","unstructured":"Aram C, Karami L, Ranjbar MM (2025) Development of a candidate mRNA vaccine based on Multi-Peptide targeting VP4 of rotavirus A: an immunoinformatics and molecular dynamics approach. Sci Rep 15(1):22610","journal-title":"Sci Rep"},{"key":"1565_CR14","doi-asserted-by":"crossref","unstructured":"Arshad SF, Rehana R, Saleem MA, Usman M, Arshad HJ, Rizwana R, Shakeela S, Rukh AS, Khan IA, Hayssam MA, Anwar M (2024) Multi-epitopes vaccine design for surface glycoprotein against SARS-CoV-2 using immunoinformatic approach. Heliyon 10(2)","DOI":"10.1016\/j.heliyon.2024.e24186"},{"issue":"2","key":"1565_CR15","doi-asserted-by":"publisher","first-page":"e0245072","DOI":"10.1371\/journal.pone.0245072","volume":"16","author":"UA Ashfaq","year":"2021","unstructured":"Ashfaq UA, Saleem S, Masoud MS, Ahmad M, Nahid N, Bhatti R, Almatroudi A, Khurshid M (2021) Rational design of multi epitope-based subunit vaccine by exploring MERS-COV proteome: Reverse vaccinology and molecular docking approach. PLoS ONE 16(2):e0245072","journal-title":"PLoS ONE"},{"key":"1565_CR16","doi-asserted-by":"crossref","unstructured":"Asim MN, Asif T, Hassan F, Dengel A (2025) Protein sequence analysis landscape: A systematic review of task types, databases, datasets, word embeddings methods, and language models. Database 2025:baaf027","DOI":"10.1093\/database\/baaf027"},{"key":"1565_CR17","doi-asserted-by":"crossref","unstructured":"Babaei M, Shahbazi B, Sarkoohi P, Azadi A, Ranjbar KJ, Ahmadi K (2026) Immunoinformatic design of a multi-epitope vaccine candidate targeting multidrug-resistant Pseudomonas aeruginosa. BMC Immunol","DOI":"10.1186\/s12865-026-00853-5"},{"issue":"5","key":"1565_CR18","doi-asserted-by":"publisher","first-page":"324","DOI":"10.2174\/0929866526666190228162751","volume":"26","author":"P Baindara","year":"2019","unstructured":"Baindara P, Mandal SM (2019) Antimicrobial peptides and vaccine development to control multi-drug resistant bacteria. Protein Pept Lett 26(5):324\u2013331","journal-title":"Protein Pept Lett"},{"issue":"4","key":"1565_CR19","doi-asserted-by":"publisher","first-page":"872","DOI":"10.1002\/pro.3805","volume":"29","author":"X Benjin","year":"2020","unstructured":"Benjin X, Ling L (2020) Developments, applications, and prospects of cryo-electron microscopy. Protein Sci 29(4):872\u2013882","journal-title":"Protein Sci"},{"issue":"10","key":"1565_CR20","doi-asserted-by":"publisher","first-page":"1161","DOI":"10.1002\/prot.26703","volume":"92","author":"K Bhattacharya","year":"2024","unstructured":"Bhattacharya K, Chanu NR, Jha SK, Khanal P, Paudel KR (2024) In silico design and evaluation of a multiepitope vaccine targeting the nucleoprotein of Puumala orthohantavirus. Proteins Struct Funct Bioinf 92(10):1161\u20131176","journal-title":"Proteins Struct Funct Bioinf"},{"key":"1565_CR21","doi-asserted-by":"publisher","DOI":"10.1016\/j.biologicals.2024.101782","volume":"87","author":"R Biswas","year":"2024","unstructured":"Biswas R, Swetha RG, Basu S, Roy A, Ramaiah S, Anbarasu A (2024) Designing multi-epitope vaccine against human cytomegalovirus integrating pan-genome and reverse vaccinology pipelines. Biologicals 87:101782. https:\/\/doi.org\/10.1016\/j.biologicals.2024.101782","journal-title":"Biologicals"},{"issue":"1","key":"1565_CR22","doi-asserted-by":"publisher","DOI":"10.3390\/molecules28010175","volume":"28","author":"C Blanes-Mira","year":"2022","unstructured":"Blanes-Mira C, Fern\u00e1ndez-Aguado P, de Andr\u00e9s-L\u00f3pez J, Fern\u00e1ndez-Carvajal A, Ferrer-Montiel A, Fern\u00e1ndez-Ballester G (2022) Comprehensive survey of consensus docking for high-throughput virtual screening. Molecules 28(1):175","journal-title":"Molecules"},{"issue":"2","key":"1565_CR23","doi-asserted-by":"publisher","first-page":"140","DOI":"10.3390\/pharmaceutics13020140","volume":"13","author":"A Bouazzaoui","year":"2021","unstructured":"Bouazzaoui A, Abdellatif AAH, Al-Allaf FA, Bogari NM, Al-Dehlawi S, Qari SH (2021) Strategies for vaccination: conventional vaccine approaches versus new-generation strategies in combination with adjuvants. Pharmaceutics 13(2):140","journal-title":"Pharmaceutics"},{"issue":"1","key":"1565_CR24","doi-asserted-by":"publisher","first-page":"63","DOI":"10.5114\/bta\/201461","volume":"106","author":"EKB Bragais III","year":"2025","unstructured":"Bragais EKB, Heralde FM III, Fernandez KCJ, Caoili SEC, Herrera-Ong LR (2025) In silico screening and identification of CTL and HTL epitopes in the secreted virulence factors of Mycobacterium tuberculosis. BioTechnologia 106(1):63\u201376. https:\/\/doi.org\/10.5114\/bta\/201461","journal-title":"BioTechnologia"},{"issue":"10","key":"1565_CR25","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1002\/jcc.21287","volume":"30","author":"BR Brooks III","year":"2009","unstructured":"Brooks BR, Brooks CL III, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30(10):1545\u20131614","journal-title":"J Comput Chem"},{"key":"1565_CR26","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-8-361","volume":"8","author":"HH Bui","year":"2007","unstructured":"Bui HH, Sidney J, Li W, Fusseder N, Sette A (2007) Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics 8:361. https:\/\/doi.org\/10.1186\/1471-2105-8-361","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"1565_CR27","doi-asserted-by":"publisher","first-page":"82","DOI":"10.37349\/ei.2023.00091","volume":"3","author":"I Carri","year":"2023","unstructured":"Carri I, Schwab E, Podaza E, Garcia Alvarez HM, Mordoh J, Nielsen M, Barrio MM (2023) Beyond MHC binding: immunogenicity prediction tools to refine neoantigen selection in cancer patients. Explor Immunol 3(2):82\u2013103","journal-title":"Explor Immunol"},{"key":"1565_CR28","doi-asserted-by":"crossref","unstructured":"Chakraborty C, Sharma AR, Bhattacharya M, Sharma G, Lee SS (2021) Immunoinformatics approach for the identification and characterization of T cell and B cell epitopes towards the peptide-based vaccine against SARS-CoV-2. Arch Med Res 52(4):362","DOI":"10.1016\/j.arcmed.2021.01.004"},{"issue":"4","key":"1565_CR29","doi-asserted-by":"publisher","first-page":"2303","DOI":"10.1007\/s10989-021-10254-4","volume":"27","author":"C Chakraborty","year":"2021","unstructured":"Chakraborty C, Sharma AR, Bhattacharya M, Lee SS (2021) Lessons learned from cutting-edge immunoinformatics on next-generation COVID-19 vaccine research. Int J Pept Res Ther 27(4):2303\u20132311. https:\/\/doi.org\/10.1007\/s10989-021-10254-4","journal-title":"Int J Pept Res Ther"},{"issue":"14","key":"1565_CR30","doi-asserted-by":"publisher","first-page":"6971","DOI":"10.3390\/ijms26146971","volume":"26","author":"S Chansap","year":"2025","unstructured":"Chansap S, Cheukamud W, Suthisintong T, Kueakhai P, Changklungmoa N (2025) Design of a multi-epitope vaccine based on Fasciola gigantica cathepsin B and evaluation of immunological responses in mice. Int J Mol Sci 26(14):6971","journal-title":"Int J Mol Sci"},{"issue":"9","key":"1565_CR31","doi-asserted-by":"publisher","first-page":"4235","DOI":"10.4049\/jimmunol.1103640","volume":"188","author":"FA Chaves","year":"2012","unstructured":"Chaves FA, Lee AH, Nayak JL, Richards KA, Sant AJ (2012) The utility and limitations of current web-available algorithms to predict peptides recognized by CD4 T cells in response to pathogen infection. J Immunol 188(9):4235\u201348. https:\/\/doi.org\/10.4049\/jimmunol.1103640","journal-title":"J Immunol"},{"issue":"20","key":"1565_CR32","doi-asserted-by":"publisher","first-page":"6929","DOI":"10.1039\/D1SC01203G","volume":"12","author":"J Chen","year":"2021","unstructured":"Chen J, Gao K, Wang R, Wei GW (2021) Prediction and mitigation of mutation threats to COVID-19 vaccines and antibody therapies. Chem Sci 12(20):6929\u20136948","journal-title":"Chem Sci"},{"issue":"10","key":"1565_CR33","doi-asserted-by":"publisher","first-page":"1357","DOI":"10.1016\/j.addr.2012.09.039","volume":"65","author":"X Chen","year":"2013","unstructured":"Chen X, Zaro JL, Shen WC (2013) Fusion protein linkers: property, design and functionality. Adv Drug Deliv Rev 65(10):1357\u201369. https:\/\/doi.org\/10.1016\/j.addr.2012.09.039","journal-title":"Adv Drug Deliv Rev"},{"key":"1565_CR34","doi-asserted-by":"publisher","first-page":"1402963","DOI":"10.3389\/fmicb.2024.1402963","volume":"15","author":"Y Chen","year":"2024","unstructured":"Chen Y, Song X, Chen W, Zhao X, Yang L, Liu D (2024) Epitope screening and self-assembled nanovaccine molecule design of PDCoV-S protein based on immunoinformatics. Front Microbiol 15:1402963","journal-title":"Front Microbiol"},{"issue":"3","key":"1565_CR35","doi-asserted-by":"publisher","first-page":"btae139","DOI":"10.1093\/bioinformatics\/btae139","volume":"40","author":"Y Chen","year":"2024","unstructured":"Chen Y, Zhang H, Wang W, Shen Y, Ping Z (2024) Rapid generation of high-quality structure figures for publication with PyMOL-PUB. Bioinformatics 40(3):btae139","journal-title":"Bioinformatics"},{"issue":"1","key":"1565_CR36","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-52223-z","volume":"14","author":"A Choudhury","year":"2024","unstructured":"Choudhury A, Kumar P, Nafidi H-A, Almaary KS, Wondmie GF, Kumar A, Bourhia M (2024a) Immunoinformatics approaches in developing a novel multi-epitope chimeric vaccine protective against Saprolegnia parasitica. Sci Rep 14(1):2260","journal-title":"Sci Rep"},{"issue":"1","key":"1565_CR37","doi-asserted-by":"publisher","first-page":"2260","DOI":"10.1038\/s41598-024-52223-z","volume":"14","author":"A Choudhury","year":"2024","unstructured":"Choudhury A, Kumar P, Nafidi HA, Almaary KS, Wondmie GF, Kumar A, Bourhia M (2024b) Immunoinformatics approaches in developing a novel multi-epitope chimeric vaccine protective against Saprolegnia parasitica. Sci Rep 14(1):2260","journal-title":"Sci Rep"},{"issue":"12","key":"1565_CR38","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4497","volume":"31","author":"JN Clifford","year":"2022","unstructured":"Clifford JN, H\u00f8ie MH, Deleuran S, Peters B, Nielsen M, Marcatili P (2022a) BepiPred-3.0: improved B-cell epitope prediction using protein language models. Protein Sci 31(12):e4497. https:\/\/doi.org\/10.1002\/pro.4497","journal-title":"Protein Sci"},{"issue":"12","key":"1565_CR39","doi-asserted-by":"publisher","first-page":"e4497","DOI":"10.1002\/pro.4497","volume":"31","author":"J Clifford","year":"2022","unstructured":"Clifford J, H\u00f8ie MH, Deleuran S, Peters B, Nielsen M, Marcatili P (2022) BepiPred-3.0: Improved B-cell epitope prediction using protein language models. Prot Sci 31(12):e4497","journal-title":"Prot Sci"},{"issue":"2","key":"1565_CR40","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1007\/s13346-021-00924-7","volume":"11","author":"C D\u2019Amico","year":"2021","unstructured":"D\u2019Amico C, Fontana F, Cheng R, Santos HA (2021) Development of vaccine formulations: past, present, and future. Drug Deliv Transl Res 11(2):353\u2013372","journal-title":"Drug Deliv Transl Res"},{"key":"1565_CR41","doi-asserted-by":"publisher","first-page":"113","DOI":"10.3389\/fimmu.2019.00113","volume":"10","author":"M Dalsass","year":"2019","unstructured":"Dalsass M, Brozzi A, Medini D, Rappuoli R (2019) Comparison of open-source reverse vaccinology programs for bacterial vaccine antigen discovery. Front Immunol 10:113","journal-title":"Front Immunol"},{"key":"1565_CR42","doi-asserted-by":"publisher","first-page":"309","DOI":"10.2147\/DDDT.S231958","volume":"14","author":"H Dana","year":"2020","unstructured":"Dana H, Mahmoodi Chalbatani G, Gharagouzloo E, Miri SR, Memari F, Rasoolzadeh R, Zinatizadeh MR, Kheirandish Zarandi P, Marmari V (2020) In silico analysis, molecular docking, molecular dynamic, cloning, expression and purification of chimeric protein in colorectal cancer treatment. Drug Des Devel Ther 14:309\u2013329","journal-title":"Drug Des Devel Ther"},{"issue":"3","key":"1565_CR43","doi-asserted-by":"publisher","first-page":"396","DOI":"10.3390\/bios13030396","volume":"13","author":"S Das","year":"2023","unstructured":"Das S, Devireddy R, Gartia MR (2023) Surface plasmon resonance (SPR) sensor for cancer biomarker detection. Biosensors 13(3):396","journal-title":"Biosensors"},{"issue":"1","key":"1565_CR44","doi-asserted-by":"publisher","first-page":"9562","DOI":"10.1038\/s41598-025-92956-z","volume":"15","author":"V Deepthi","year":"2025","unstructured":"Deepthi V, Sasikumar A, Mohanakumar KP, Rajamma U (2025) Computationally designed multi-epitope vaccine construct targeting the SARS-CoV-2 spike protein elicits robust immune responses in silico. Sci Rep 15(1):9562","journal-title":"Sci Rep"},{"key":"1565_CR45","doi-asserted-by":"crossref","unstructured":"Demissie EA, Park SY, Moon JH, Lee DY (2025) Comparative analysis of codon optimization tools: advancing toward a multi-criteria framework for synthetic gene design. J Microbiol Biotechnol 35:e2411066","DOI":"10.4014\/jmb.2411.11066"},{"key":"1565_CR46","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2022.975408","volume":"12","author":"Z Deng","year":"2022","unstructured":"Deng Z, Yang H, Tian Y, Liu Z, Sun F, Yang P (2022) An OX40L mRNA vaccine inhibits the growth of hepatocellular carcinoma. Front Oncol 12:975408. https:\/\/doi.org\/10.3389\/fonc.2022.975408","journal-title":"Front Oncol"},{"issue":"4","key":"1565_CR47","doi-asserted-by":"publisher","first-page":"569","DOI":"10.1080\/14760584.2022.2021882","volume":"21","author":"J Dey","year":"2022","unstructured":"Dey J, Mahapatra SR, Lata S, Patro S, Misra N, Suar M (2022) Exploring Klebsiella pneumoniae capsule polysaccharide proteins to design multiepitope subunit vaccine to fight against pneumonia. Expert Rev Vaccines 21(4):569\u2013587","journal-title":"Expert Rev Vaccines"},{"key":"1565_CR48","doi-asserted-by":"publisher","unstructured":"Dhanda SK, Mahajan S, Paul S, Yan Z, Kim H, Jespersen MC, Jurtz V, Andreatta M, Greenbaum JA, Marcatili P, Sette A, Nielsen M, Peters B (2019) IEDB-AR: immune epitope database-analysis resource in 2019. Nucleic Acids Res 47(W1):W502\u2013W506 https:\/\/doi.org\/10.1093\/nar\/gkz452","DOI":"10.1093\/nar\/gkz452"},{"issue":"8","key":"1565_CR49","doi-asserted-by":"publisher","first-page":"943","DOI":"10.1038\/s41587-021-00893-9","volume":"39","author":"T Dileepan","year":"2021","unstructured":"Dileepan T, Malhotra D, Kotov DI, Kolawole EM, Krueger PD, Evavold BD, Jenkins MK (2021) MHC class II tetramers engineered for enhanced binding to CD4 improve detection of antigen-specific T cells. Nat Biotechnol 39(8):943\u2013948","journal-title":"Nat Biotechnol"},{"issue":"12","key":"1565_CR50","doi-asserted-by":"publisher","first-page":"5634","DOI":"10.1038\/s41596-021-00628-9","volume":"16","author":"Z Du","year":"2021","unstructured":"Du Z, Su H, Wang W, Ye L, Wei H, Peng Z, Anishchenko I, Baker D, Yang J (2021) The trRosetta server for fast and accurate protein structure prediction. Nat Protoc 16(12):5634\u20135651","journal-title":"Nat Protoc"},{"issue":"2","key":"1565_CR51","doi-asserted-by":"publisher","first-page":"114","DOI":"10.3390\/cryst10020114","volume":"10","author":"K Elez","year":"2020","unstructured":"Elez K, Bonvin AMJJ, Vangone A (2020) Biological vs. crystallographic protein interfaces: an overview of computational approaches for their classification. Crystals 10(2):114","journal-title":"Crystals"},{"issue":"1","key":"1565_CR52","doi-asserted-by":"publisher","first-page":"11951","DOI":"10.1038\/s41598-024-61991-7","volume":"14","author":"A Elrashedy","year":"2024","unstructured":"Elrashedy A, Nayel M, Salama A, Salama MM, Hasan ME (2024) Bioinformatics approach for structure modeling, vaccine design, and molecular docking of Brucella candidate proteins BvrR, OMP25, and OMP31. Sci Rep 14(1):11951","journal-title":"Sci Rep"},{"key":"1565_CR53","doi-asserted-by":"publisher","first-page":"931","DOI":"10.1016\/B978-0-12-809633-8.20469-X","volume-title":"Encyclopedia of Bioinformatics and Computational Biology","author":"CLP Eng","year":"2019","unstructured":"Eng CLP, Tan TW, Tong JC (2019) Immunoinformatics Databases. In: Ranganathan S, Gribskov M, Nakai K, Sch\u00f6nbach C (eds) Encyclopedia of Bioinformatics and Computational Biology. Academic Press, Oxford, pp 931\u2013939"},{"key":"1565_CR54","doi-asserted-by":"publisher","unstructured":"Eyig\u00fcn CP, Yilmaz S, G\u00fcl C, Seng\u00fcl A, Hacibektasoglu A, Van Thiel DH (1998) A comparative trial of two surface subunit recombinant hepatitis B vaccines vs a surface and PreS subunit vaccine for immunization of healthy adults. J Viral Hepat 5(4):265\u2013269 https:\/\/doi.org\/10.1046\/j.1365-2893.1998.00106.x","DOI":"10.1046\/j.1365-2893.1998.00106.x"},{"issue":"5","key":"1565_CR55","doi-asserted-by":"publisher","first-page":"819","DOI":"10.3390\/vaccines10050819","volume":"10","author":"A Di Facciol\u00e0","year":"2022","unstructured":"Facciol\u00e0 A, Visalli G, Lagan\u00e0 A, Di Pietro A (2022) An overview of vaccine adjuvants: current evidence and future perspectives. Vaccines 10(5):819","journal-title":"Vaccines"},{"issue":"5","key":"1565_CR56","doi-asserted-by":"publisher","first-page":"2550014","DOI":"10.1142\/s0219720025500143","volume":"23","author":"MK Fath","year":"2025","unstructured":"Fath MK (2025) The novel design of a multi-epitope vaccine candidate against the dengue virus using advanced immunoinformatics and structural analysis. J Bioinform Comput Biol 23(5):2550014. https:\/\/doi.org\/10.1142\/s0219720025500143","journal-title":"J Bioinform Comput Biol"},{"issue":"6","key":"1565_CR57","doi-asserted-by":"publisher","first-page":"3210","DOI":"10.3390\/ijms22063210","volume":"22","author":"KA Galanis","year":"2021","unstructured":"Galanis KA, Nastou KC, Papandreou NC, Petichakis GN, Pigis DG, Iconomidou VA (2021) Linear B-cell epitope prediction for in silico vaccine design: A performance review of methods available via command-line interface. Int J Mol Sci 22(6):3210","journal-title":"Int J Mol Sci"},{"issue":"6","key":"1565_CR58","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1007\/s10719-022-10083-7","volume":"39","author":"BS Gandhamaneni","year":"2022","unstructured":"Gandhamaneni BS, Krishnamoorthy HR, Veerappapillai S, Mohapatra SR, Karuppasamy R (2022) Envelope Glycoprotein based multi-epitope vaccine against a co-infection of Human Herpesvirus 5 and Human Herpesvirus 6 using in silico strategies. Glycoconj J 39(6):711\u2013724","journal-title":"Glycoconj J"},{"issue":"6","key":"1565_CR59","doi-asserted-by":"publisher","first-page":"129","DOI":"10.14745\/ccdr.v44i06a02","volume":"44","author":"I Gemmill","year":"2018","unstructured":"Gemmill I, Young K (2018) Summary of the NACI literature review on the comparative effectiveness of subunit and split virus inactivated influenza vaccines in older adults. Can Commun Dis Rep 44(6):129\u2013133. https:\/\/doi.org\/10.14745\/ccdr.v44i06a02","journal-title":"Can Commun Dis Rep"},{"issue":"2","key":"1565_CR60","doi-asserted-by":"publisher","first-page":"81","DOI":"10.7774\/cevr.2020.9.2.81","volume":"9","author":"AD Ghaffari","year":"2020","unstructured":"Ghaffari AD, Dalimi A, Ghaffarifar F, Pirestani M (2020) Antigenic properties of dense granule antigen 12 protein using bioinformatics tools in order to improve vaccine design against Toxoplasma gondii. Clin Exp Vaccine Res 9(2):81\u201396","journal-title":"Clin Exp Vaccine Res"},{"key":"1565_CR61","doi-asserted-by":"crossref","unstructured":"Ghasemi JB, Abdolmaleki A, Shiri F (2016) Molecular docking challenges and limitations","DOI":"10.4018\/978-1-5225-0362-0.ch003"},{"issue":"12","key":"1565_CR62","doi-asserted-by":"publisher","first-page":"1490","DOI":"10.3390\/vaccines9121490","volume":"9","author":"M Ghattas","year":"2021","unstructured":"Ghattas M, Dwivedi G, Lavertu M, Alameh MG (2021) Vaccine technologies and platforms for infectious diseases: current progress, challenges, and opportunities. Vaccines 9(12):1490","journal-title":"Vaccines"},{"key":"1565_CR63","doi-asserted-by":"publisher","first-page":"126756","DOI":"10.1016\/j.vaccine.2025.126756","volume":"48","author":"N Gloanec","year":"2025","unstructured":"Gloanec N, Guyard-Nicod\u00e8me M, Chemaly M, Dory D (2025) Reverse vaccinology: A strategy also used for identifying potential vaccine antigens in poultry. Vaccine 48:126756","journal-title":"Vaccine"},{"key":"1565_CR64","doi-asserted-by":"publisher","first-page":"906","DOI":"10.1016\/B978-0-12-809633-8.20452-4","volume-title":"Encyclopedia of Bioinformatics and Computational Biology","author":"M G\u00f3mez Perosanz","year":"2019","unstructured":"G\u00f3mez Perosanz M, Russo G, Sanchez-Trincado Lopez JL, Pennisi M, Reche PA, Shepherd A, Pappalardo F (2019) Computational Immunogenetics. In: Ranganathan S, Gribskov M, Nakai K, Sch\u00f6nbach C (eds) Encyclopedia of Bioinformatics and Computational Biology. Academic Press, Oxford, pp 906\u2013930"},{"key":"1565_CR65","doi-asserted-by":"publisher","DOI":"10.1093\/femsre\/fuad004","author":"SJ Goodswen","year":"2023","unstructured":"Goodswen SJ, Kennedy PJ, Ellis JT (2023a) A guide to current methodology and usage of reverse vaccinology towards in silico vaccine discovery. FEMS Microbiol Rev. https:\/\/doi.org\/10.1093\/femsre\/fuad004","journal-title":"FEMS Microbiol Rev"},{"key":"1565_CR66","doi-asserted-by":"crossref","unstructured":"Goodswen SJ, Kennedy PJ, Ellis JT (2023b) A guide to current methodology and usage of reverse vaccinology towards in silico vaccine discovery. FEMS Microbiol Rev 47(2):fuad004","DOI":"10.1093\/femsre\/fuad004"},{"key":"1565_CR67","doi-asserted-by":"crossref","unstructured":"Grote A, Hiller K, Scheer M, M\u00fcnch R, N\u00f6rtemann B, Hempel DC, Jahn D (2005) JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res 33(suppl_2):W526\u2013W531","DOI":"10.1093\/nar\/gki376"},{"issue":"16","key":"1565_CR68","doi-asserted-by":"publisher","first-page":"5315","DOI":"10.1021\/acs.jctc.3c00513","volume":"19","author":"F Guarra","year":"2023","unstructured":"Guarra F, Colombo G (2023) Computational methods in immunology and vaccinology: design and development of antibodies and immunogens. J Chem Theory Comput 19(16):5315\u20135333","journal-title":"J Chem Theory Comput"},{"key":"1565_CR69","doi-asserted-by":"crossref","unstructured":"Gupta PK, Chaudhary J, Gautam T (2024) Bioinformatics for gene identification and crop improvement in wheat. In: Chen JT (ed) Bioinformatics for plant research and crop breeding. Wiley, pp 321\u2013349","DOI":"10.1002\/9781394209965.ch14"},{"issue":"7","key":"1565_CR70","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1016\/j.tibtech.2004.04.006","volume":"22","author":"C Gustafsson","year":"2004","unstructured":"Gustafsson C, Govindarajan S, Minshull J (2004) Codon bias and heterologous protein expression. Trends Biotechnol 22(7):346\u2013353","journal-title":"Trends Biotechnol"},{"issue":"3","key":"1565_CR71","doi-asserted-by":"publisher","first-page":"735","DOI":"10.1093\/bioinformatics\/btz670","volume":"36","author":"MBB Gutierres","year":"2020","unstructured":"Gutierres MBB, Bonorino CBC, Rigo MM (2020) ChaperISM: improved chaperone binding prediction using position-independent scoring matrices. Bioinformatics 36(3):735\u2013741","journal-title":"Bioinformatics"},{"issue":"4","key":"1565_CR72","doi-asserted-by":"publisher","first-page":"3705","DOI":"10.3390\/cimb45040240","volume":"45","author":"D Gutnik","year":"2023","unstructured":"Gutnik D, Evseev P, Miroshnikov K, Shneider M (2023) Using AlphaFold predictions in viral research. Curr Issues Mol Biol 45(4):3705\u20133732. https:\/\/doi.org\/10.3390\/cimb45040240","journal-title":"Curr Issues Mol Biol"},{"issue":"1","key":"1565_CR73","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-025-04124-y","volume":"25","author":"TU Habiba","year":"2025","unstructured":"Habiba TU, Hussain Z, Asghar F, Nawaz W (2025a) Reverse vaccinology-based identification and in silico characterization of immunogenic membrane proteins of Salmonella Typhimurium as novel vaccine targets against multidrug-resistant infections. BMC Microbiol 25(1):542. https:\/\/doi.org\/10.1186\/s12866-025-04124-y","journal-title":"BMC Microbiol"},{"issue":"1","key":"1565_CR74","doi-asserted-by":"publisher","first-page":"542","DOI":"10.1186\/s12866-025-04124-y","volume":"25","author":"TU Habiba","year":"2025","unstructured":"Habiba TU, Hussain Z, Asghar F, Nawaz W (2025b) Reverse vaccinology-based identification and in silico characterization of immunogenic membrane proteins of Salmonella Typhimurium as novel vaccine targets against multidrug-resistant infections. BMC Microbiol 25(1):542","journal-title":"BMC Microbiol"},{"issue":"4","key":"1565_CR75","doi-asserted-by":"publisher","first-page":"e1007449","DOI":"10.1371\/journal.pcbi.1007449","volume":"16","author":"Y Haddad","year":"2020","unstructured":"Haddad Y, Adam V, Heger Z (2020) Ten quick tips for homology modeling of high-resolution protein 3D structures. PLoS Comput Biol 16(4):e1007449","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"1565_CR76","doi-asserted-by":"publisher","first-page":"1159","DOI":"10.1007\/s00253-020-11054-4","volume":"105","author":"A Hajialibeigi","year":"2021","unstructured":"Hajialibeigi A, Amani J, Gargari SLM (2021) Identification and evaluation of novel vaccine candidates against Shigella flexneri through reverse vaccinology approach. Appl Microbiol Biotechnol 105(3):1159\u20131173","journal-title":"Appl Microbiol Biotechnol"},{"issue":"20","key":"1565_CR77","doi-asserted-by":"publisher","first-page":"167093","DOI":"10.1016\/j.jmb.2021.167093","volume":"433","author":"MK Higgins","year":"2021","unstructured":"Higgins MK (2021) Can we AlphaFold our way out of the next pandemic? J Mol Biol 433(20):167093. https:\/\/doi.org\/10.1016\/j.jmb.2021.167093","journal-title":"J Mol Biol"},{"key":"1565_CR78","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2023.1192385","volume":"14","author":"D Hu","year":"2023","unstructured":"Hu D, Irving AT (2023) Massively-multiplexed epitope mapping techniques for viral antigen discovery. Front Immunol 14:1192385. https:\/\/doi.org\/10.3389\/fimmu.2023.1192385","journal-title":"Front Immunol"},{"key":"1565_CR79","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1016\/B978-012361160-4\/50066-9","volume-title":"Matthews\u2019 Plant Virology (Fourth Edition)","author":"R Hull","year":"2002","unstructured":"Hull R (2002) CHAPTER 15 - Methods for Assay, Detection and Diagnosis. In: Hull R (ed) Matthews\u2019 Plant Virology (Fourth Edition). Academic Press, London, pp 627\u2013674"},{"issue":"14_suppl","key":"1565_CR80","doi-asserted-by":"publisher","first-page":"2525","DOI":"10.1200\/jco.2004.22.90140.2525","volume":"22","author":"GY Ishioka","year":"2004","unstructured":"Ishioka GY, Disis ML, Morse MA, Cunningham CC, Lenz H-J, Figlin RA, Chesnut RW, Fikes J (2004) A phase I trial of a multi-epitope cancer vaccine (EP-2101) in non-small cell lung (NSCLC) and colon cancer patients. J Clin Oncol 22(14_suppl):2525\u20132525","journal-title":"J Clin Oncol"},{"key":"1565_CR81","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1007\/978-1-0716-3985-6_17","volume-title":"Protein-Protein Docking: Methods and Protocols","author":"MK Jastrz\u0119bski","year":"2024","unstructured":"Jastrz\u0119bski MK (2024) Computational Methods to Target Protein-Protein Interactions. Protein-Protein Docking: Methods and Protocols. Springer, pp 327\u2013343"},{"key":"1565_CR82","doi-asserted-by":"crossref","unstructured":"Javaid M, Sagheer M, Saleem MZ, Hussain N, Munawar N (2025) Immunotherapeutic approach for improving the efficacy of a novel subunit vaccine against SARS-CoV-2 by cytotoxic T-lymphocytes (CTL) epitopes. Scientifica 2025:6025826","DOI":"10.1155\/sci5\/6025826"},{"key":"1565_CR83","doi-asserted-by":"publisher","first-page":"1280299","DOI":"10.3389\/fimmu.2023.1280299","volume":"14","author":"F Jiang","year":"2023","unstructured":"Jiang F, Han Y, Liu Y, Xue Y, Cheng P, Xiao L, Gong W (2023) A comprehensive approach to developing a multi-epitope vaccine against Mycobacterium tuberculosis: from in silico design to in vitro immunization evaluation. Front Immunol 14:1280299","journal-title":"Front Immunol"},{"issue":"6","key":"1565_CR84","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1107\/S2059798322002741","volume":"78","author":"G Jones","year":"2022","unstructured":"Jones G, Jindal A, Ghani U, Kotelnikov S, Egbert M, Hashemi N, Vajda S, Padhorny D, Kozakov D (2022) Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap. Acta Crystallogr D Struct Biol 78(6):690\u2013697","journal-title":"Acta Crystallogr D Struct Biol"},{"issue":"7","key":"1565_CR85","doi-asserted-by":"publisher","first-page":"2766","DOI":"10.18203\/2394-6040.ijcmph20182419","volume":"5","author":"KP Joshi","year":"2018","unstructured":"Joshi KP, Padugupati S, Robins M (2018) Assessment of educational outcomes of small group discussion versus traditional lecture format among undergraduate medical students. Int J Community Med Public Health 5(7):2766\u20132769","journal-title":"Int J Community Med Public Health"},{"issue":"23","key":"1565_CR86","doi-asserted-by":"publisher","first-page":"4567","DOI":"10.1093\/bioinformatics\/btab687","volume":"37","author":"V Junet","year":"2021","unstructured":"Junet V, Daura X (2021) CNN-PepPred: an open-source tool to create convolutional NN models for the discovery of patterns in peptide sets\u2014application to peptide\u2013MHC class II binding prediction. Bioinformatics 37(23):4567\u20134568","journal-title":"Bioinformatics"},{"key":"1565_CR87","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1016\/j.compbiolchem.2018.05.007","volume":"75","author":"T Kakati","year":"2018","unstructured":"Kakati T, Ahmed HA, Bhattacharyya DK, Kalita JK (2018) THD-Tricluster: A robust triclustering technique and its application in condition specific change analysis in HIV-1 progression data. Comput Biol Chem 75:154\u2013167","journal-title":"Comput Biol Chem"},{"issue":"4","key":"1565_CR88","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1016\/j.vaccine.2011.11.088","volume":"30","author":"SK Kanagavelu","year":"2012","unstructured":"Kanagavelu SK, Snarsky V, Termini JM, Gupta S, Barzee S, Wright JA, Khan WN, Kornbluth RS, Stone GW (2012) Soluble multi-trimeric TNF superfamily ligand adjuvants enhance immune responses to a HIV-1 Gag DNA vaccine. Vaccine 30(4):691\u2013702. https:\/\/doi.org\/10.1016\/j.vaccine.2011.11.088","journal-title":"Vaccine"},{"issue":"2","key":"1565_CR89","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1080\/08830185.2021.1960986","volume":"42","author":"D Kandari","year":"2023","unstructured":"Kandari D, Bhatnagar R (2023) Antibody engineering and its therapeutic applications. Int Rev Immunol 42(2):156\u2013183","journal-title":"Int Rev Immunol"},{"issue":"10","key":"1565_CR90","doi-asserted-by":"publisher","first-page":"4404","DOI":"10.3390\/ijms27104404","volume":"27","author":"P Kannan","year":"2026","unstructured":"Kannan P, Nanda Kumar MP, Nanda Kumar SK, Vasudevan V, Kaviarasan K, Ramasamy M (2026) Molecular modeling of N-acetylglucosamine binding to the I154R mutant of NAGLU: pathogenic insights into Sanfilippo syndrome type B. Int J Mol Sci 27(10):4404","journal-title":"Int J Mol Sci"},{"issue":"1","key":"1565_CR91","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1007\/s10735-025-10704-z","volume":"57","author":"V Karthick","year":"2026","unstructured":"Karthick V, Amalraj S, Thamarai R, Paventhan S (2026) Molecular docking in histological biomarker discovery and disease modeling: techniques, validation, and translational perspectives. J Mol Histol 57(1):28","journal-title":"J Mol Histol"},{"key":"1565_CR92","doi-asserted-by":"crossref","unstructured":"Kathwate GH (2022) In silico design and characterization of multi-epitopes vaccine for SARS-CoV2 from its spike protein. Int J Pept Res Ther 28(1):37","DOI":"10.1007\/s10989-021-10348-z"},{"issue":"7","key":"1565_CR93","doi-asserted-by":"publisher","first-page":"2028","DOI":"10.3390\/biomedicines11072028","volume":"11","author":"H Kaur","year":"2023","unstructured":"Kaur H, Modgil V, Chaudhary N, Mohan B, Taneja N (2023) Computational guided drug targets identification against extended-spectrum beta-lactamase-producing multi-drug resistant uropathogenic Escherichia coli. Biomedicines 11(7):2028","journal-title":"Biomedicines"},{"key":"1565_CR94","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1002\/9783527840748.ch10","volume":"1","author":"TF Kellici","year":"2024","unstructured":"Kellici TF, Hristozov D, Morao I (2024) AI-based protein structure predictions and their implications in drug discovery. Comput Drug Discov Methods Appl 1:227\u2013253","journal-title":"Comput Drug Discov Methods Appl"},{"key":"1565_CR95","doi-asserted-by":"publisher","unstructured":"Khalaj A, Moghri SAHMH (2025a) Immunoinformatics design of multi-epitope vaccine candidates against \"ESKAPE\" pathogens as nosocomial infection. Comput Biol Med 197(pt B):111100 https:\/\/doi.org\/10.1016\/j.compbiomed.2025.111100","DOI":"10.1016\/j.compbiomed.2025.111100"},{"key":"1565_CR96","doi-asserted-by":"publisher","first-page":"111100","DOI":"10.1016\/j.compbiomed.2025.111100","volume":"197","author":"A Khalaj","year":"2025","unstructured":"Khalaj A, Moghri SAHMH (2025b) Immunoinformatics design of multi-epitope vaccine candidates against ESKAPE pathogens as nosocomial infection. Comput Biol Med 197:111100. https:\/\/doi.org\/10.1016\/j.compbiomed.2025.111100","journal-title":"Comput Biol Med"},{"issue":"7","key":"1565_CR97","doi-asserted-by":"publisher","first-page":"1264","DOI":"10.3390\/vaccines11071264","volume":"11","author":"K Khalid","year":"2023","unstructured":"Khalid K, Poh CL (2023) The promising potential of reverse vaccinology-based next-generation vaccine development over conventional vaccines against antibiotic-resistant bacteria. Vaccines 11(7):1264. https:\/\/doi.org\/10.3390\/vaccines11071264","journal-title":"Vaccines"},{"issue":"1","key":"1565_CR98","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s12033-024-01358-5","volume":"68","author":"K Khalid","year":"2026","unstructured":"Khalid K, Ahmad F, Anwar A, Ong SK (2026) A bibliometric analysis on multi-epitope vaccine development against SARS-CoV-2: Current status, development, and future directions. Mol Biotechnol 68(1):1\u201322","journal-title":"Mol Biotechnol"},{"issue":"1","key":"1565_CR99","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1007\/s10989-021-10316-7","volume":"28","author":"K Khalid","year":"2022","unstructured":"Khalid K, Irum S, Ullah SR, Andleeb S (2022) In-silico vaccine design based on a novel vaccine candidate against infections caused by Acinetobacter baumannii. Int J Pept Res Ther 28(1):16","journal-title":"Int J Pept Res Ther"},{"key":"1565_CR100","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines11061090","author":"NA Khamjan","year":"2023","unstructured":"Khamjan NA, Lohani M, Khan MF, Khan S, Algaissi A (2023) Immunoinformatics strategy to develop a novel universal multiple epitope-based COVID-19 vaccine. Vaccines. https:\/\/doi.org\/10.3390\/vaccines11061090","journal-title":"Vaccines"},{"issue":"1","key":"1565_CR101","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1186\/s12860-023-00484-3","volume":"24","author":"I Khater","year":"2023","unstructured":"Khater I, Nassar A (2023) A computational peptide model induces cancer cells\u2019 apoptosis by docking Kringle 5 to GRP78. BMC Mol Cell Biol 24(1):25","journal-title":"BMC Mol Cell Biol"},{"issue":"11","key":"1565_CR102","doi-asserted-by":"publisher","first-page":"2574","DOI":"10.3390\/microorganisms13112574","volume":"13","author":"SH Kim","year":"2025","unstructured":"Kim SH, Min YH, Park MC (2025) Antimicrobial peptides: current status, mechanisms of action, and strategies to overcome therapeutic limitations. Microorganisms 13(11):2574","journal-title":"Microorganisms"},{"key":"1565_CR103","doi-asserted-by":"publisher","first-page":"111095","DOI":"10.1016\/j.rineng.2026.111095","volume":"30","author":"MZ Kinde","year":"2026","unstructured":"Kinde MZ, Gessese AT, Fenta MD, Chanie SD, Sisay T (2026) Harnessing AlphaFold: Applications in disease understanding, drug discovery, and vaccine design. Results Eng 30:111095. https:\/\/doi.org\/10.1016\/j.rineng.2026.111095","journal-title":"Results Eng"},{"key":"1565_CR104","doi-asserted-by":"publisher","DOI":"10.1016\/j.microb.2025.100320","volume":"7","author":"A Kottarathil","year":"2025","unstructured":"Kottarathil A, Murugan G, Rajkumar DS, Chandran AK, Elumalai V, Padmanaban R (2025) Designing multi-epitope-based vaccine targeting immunogenic proteins of Streptococcus mutans using immunoinformatics to prevent caries. Microbe 7:100320. https:\/\/doi.org\/10.1016\/j.microb.2025.100320","journal-title":"Microbe"},{"issue":"1","key":"1565_CR105","doi-asserted-by":"publisher","first-page":"14904","DOI":"10.1038\/s41598-018-33298-x","volume":"8","author":"EEG de Kozlova","year":"2018","unstructured":"Kozlova EEG, Cerf L, Schneider FS, Viart BT, NGuyen C, Steiner BT, de Almeida Lima S, Molina F, Duarte CG, Felicori L, Ch\u00e1vez-Ol\u00f3rtegui C, Machado-de-\u00c1vila RA (2018) Computational B-cell epitope identification and production of neutralizing murine antibodies against Atroxlysin-I. Sci Rep 8(1):14904. https:\/\/doi.org\/10.1038\/s41598-018-33298-x","journal-title":"Sci Rep"},{"key":"1565_CR106","doi-asserted-by":"publisher","first-page":"108083","DOI":"10.1016\/j.compbiomed.2024.108083","volume":"170","author":"N Kumar","year":"2024","unstructured":"Kumar N, Tripathi S, Sharma N, Patiyal S, Devi NL, Raghava GPS (2024) A method for predicting linear and conformational B-cell epitopes in an antigen from its primary sequence. Comput Biol Med 170:108083. https:\/\/doi.org\/10.1016\/j.compbiomed.2024.108083","journal-title":"Comput Biol Med"},{"issue":"4","key":"1565_CR107","doi-asserted-by":"publisher","first-page":"2094","DOI":"10.1080\/07391102.2023.2203253","volume":"42","author":"MR Lahimchi","year":"2024","unstructured":"Lahimchi MR, Madanchi H, Ahmadi K, Shahbazi B, Yousefi B (2024) In silico designing a novel TLR4-mediating multiepitope vaccine against monkeypox via advanced immunoinformatics and bioinformatics approaches. J Biomol Struct Dyn 42(4):2094\u20132110","journal-title":"J Biomol Struct Dyn"},{"issue":"1","key":"1565_CR108","doi-asserted-by":"publisher","first-page":"52","DOI":"10.1111\/imm.13907","volume":"175","author":"AR Lakra","year":"2025","unstructured":"Lakra AR (2025) X-Ray Crystallography Based Epitope Mapping of Glycoproteins and RNA in Chandipura Vesiculovirus for Vaccine Design. Immunology 175(1):52\u201366","journal-title":"Immunology"},{"issue":"5","key":"1565_CR109","doi-asserted-by":"publisher","first-page":"bbaf454","DOI":"10.1093\/bib\/bbaf454","volume":"26","author":"J Lee","year":"2025","unstructured":"Lee J, Nguyen CH, Mamitsuka H (2025) Beyond rigid docking: deep learning approaches for fully flexible protein\u2013ligand interactions. Brief Bioinform 26(5):bbaf454","journal-title":"Brief Bioinform"},{"issue":"1","key":"1565_CR110","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.bsheal.2025.01.006","volume":"7","author":"J Li","year":"2025","unstructured":"Li J, Jia T, Yang L (2025) Targeting anti-virulence factor strategies of bacterial pathogens. Biosaf Health 7(1):1\u20134","journal-title":"Biosaf Health"},{"issue":"3","key":"1565_CR111","doi-asserted-by":"publisher","first-page":"248","DOI":"10.3390\/vaccines13030248","volume":"13","author":"J Li","year":"2025","unstructured":"Li J, Ju Y, Jiang M, Li S, Yang XY (2025) Epitope-based vaccines: the next generation of promising vaccines against bacterial infection. Vaccines 13(3):248","journal-title":"Vaccines"},{"issue":"1","key":"1565_CR112","doi-asserted-by":"publisher","first-page":"19537","DOI":"10.1038\/s41598-024-70579-0","volume":"14","author":"S Li","year":"2024","unstructured":"Li S, Bai X, Wang C (2024) Epitopes screening and vaccine molecular design of PEDV S protein based on immunoinformatics. Sci Rep 14(1):19537","journal-title":"Sci Rep"},{"issue":"7","key":"1565_CR113","doi-asserted-by":"publisher","first-page":"820","DOI":"10.3390\/pharmaceutics17070820","volume":"17","author":"AN Mafe","year":"2025","unstructured":"Mafe AN, B\u00fcsselberg D (2025) Phage therapy in managing Multidrug-Resistant (MDR) infections in cancer therapy: Innovations, Complications, and future directions. Pharmaceutics 17(7):820","journal-title":"Pharmaceutics"},{"key":"1565_CR114","doi-asserted-by":"publisher","DOI":"10.1177\/11779322241287114","volume":"18","author":"SA Malgwi","year":"2024","unstructured":"Malgwi SA, Adeleke VT, Adeleke MA, Okpeku M (2024) Multi-epitope based peptide vaccine candidate against Babesia infection from rhoptry-associated protein 1 (RAP-1) antigen using immuno-informatics: an in silico approach. Bioinform Biol Insights 18:11779322241287114. https:\/\/doi.org\/10.1177\/11779322241287114","journal-title":"Bioinform Biol Insights"},{"key":"1565_CR115","doi-asserted-by":"publisher","DOI":"10.1016\/j.health.2022.100044","volume":"2","author":"DD Martinelli","year":"2022","unstructured":"Martinelli DD (2022) In silico vaccine design: a tutorial in immunoinformatics. Healthc Anal 2:100044. https:\/\/doi.org\/10.1016\/j.health.2022.100044","journal-title":"Healthc Anal"},{"key":"1565_CR116","doi-asserted-by":"crossref","unstructured":"Mathur N, Chandragiri SS, Shandily S, Santoki KM, Vadhavana NN, Shah S, Chandra M (2024) In silico docking: Protocols for computational exploration of Molecular Interactions. In: Unravelling Molecular Docking - From Theory to Practice. IntechOpen.","DOI":"10.5772\/intechopen.1005527"},{"issue":"7","key":"1565_CR117","doi-asserted-by":"publisher","first-page":"1283","DOI":"10.1021\/acsinfecdis.2c00649","volume":"9","author":"A Mayorga-Ramos","year":"2023","unstructured":"Mayorga-Ramos A, Z\u00fa\u00f1iga-Miranda J, Carrera-Pacheco SE, Barba-Ostria C, Guam\u00e1n LP (2023) CRISPR-Cas-based antimicrobials: design, challenges, and bacterial mechanisms of resistance. ACS Infect Dis 9(7):1283\u20131302. https:\/\/doi.org\/10.1021\/acsinfecdis.2c00649","journal-title":"ACS Infect Dis"},{"issue":"4","key":"1565_CR118","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1111\/tmi.13865","volume":"28","author":"IE Mba","year":"2023","unstructured":"Mba IE, Sharndama HC, Anyaegbunam NKG, Anekpo CC, Amadi BC, Morumda D, Doowuese Y, Ihezuo UJ, Chukwukelu JU, Okeke OP (2023) Vaccine development for bacterial pathogens: Advances, challenges and prospects. Trop Med Int Health 28(4):275\u2013299","journal-title":"Trop Med Int Health"},{"issue":"12","key":"1565_CR119","doi-asserted-by":"publisher","first-page":"3103","DOI":"10.1080\/21645515.2016.1216287","volume":"12","author":"S McClean","year":"2016","unstructured":"McClean S (2016) Prospects for subunit vaccines: Technology advances resulting in efficacious antigens requires matching advances in early clinical trial investment. Hum Vaccin Immunother 12(12):3103\u20133106. https:\/\/doi.org\/10.1080\/21645515.2016.1216287","journal-title":"Hum Vaccin Immunother"},{"issue":"4","key":"1565_CR120","doi-asserted-by":"publisher","DOI":"10.1002\/pro.4605","volume":"32","author":"M Mendes","year":"2023","unstructured":"Mendes M, Mahita J, Blazeska N, Greenbaum J, Ha B, Wheeler K, Wang J, Shackelford D, Sette A, Peters B (2023) IEDB-3D 2.0: structural data analysis within the Immune Epitope Database. Protein Sci 32(4):e4605. https:\/\/doi.org\/10.1002\/pro.4605","journal-title":"Protein Sci"},{"key":"1565_CR121","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1201\/9781032721811-20","volume-title":"Emerging and Re-Emerging Viral Diseases","author":"SK Mishra","year":"2025","unstructured":"Mishra SK, Kalathiya U, Padariya M, Georrge JJ (2025) Role of Bioinformatics in Emerging and Re-Emerging Infectious Diseases: A Drug and Vaccine Development Prospective. Emerging and Re-Emerging Viral Diseases. CRC Press, pp 266\u2013274"},{"key":"1565_CR122","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1016\/B978-0-443-13395-4.00001-0","volume-title":"Reverse Vaccinology","author":"SK Mishra","year":"2024","unstructured":"Mishra SK, Pandya M, Bhatt T, Georrge JJ (2024) Chapter 11 - Reverse vaccinology 2.0: computational resources for B-cell epitope prediction. In: Das J, Dave S, de Castro Soares S, Tiwari S (eds) Reverse Vaccinology. Academic Press, pp 203\u2013216"},{"key":"1565_CR123","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1016\/B978-0-443-13395-4.00003-4","volume-title":"Reverse Vaccinology","author":"SK Mishra","year":"2024","unstructured":"Mishra SK, Georrge JJ (2024) Chapter 9 - Tools and platform for allergenicity prediction. In: Das J, Dave S, Soares SdC, Tiwari S (eds) Reverse Vaccinology. Academic Press, pp 165\u2013178"},{"key":"1565_CR124","first-page":"1","volume-title":"Frontiers in Anti-Infective Agents: Volume 6","author":"A Mitra","year":"2021","unstructured":"Mitra A (2021) Reverse vaccinology approaches for rapid vaccine design against emerging infectious diseases. Frontiers in Anti-Infective Agents: Volume 6. Bentham Science Publishers, pp 1\u201318"},{"issue":"2","key":"1565_CR125","doi-asserted-by":"publisher","DOI":"10.1093\/nargab\/lqaf058","volume":"7","author":"Q Mu","year":"2025","unstructured":"Mu Q, Yu G, Zhou G, He Y, Zhang J (2025) DRBP-EDP: classification of DNA-binding proteins and RNA-binding proteins using ESM-2 and dual-path neural network. NAR Genom Bioinform 7(2):lqaf058","journal-title":"NAR Genom Bioinform"},{"key":"1565_CR126","doi-asserted-by":"crossref","unstructured":"Mursal M, Ahmad M, Hussain S, Khan MF (2024) Navigating the computational seas: a comprehensive overview of molecular docking software in drug discovery. In: Unravelling Molecular Docking - From Theory to Practice. IntechOpen.","DOI":"10.5772\/intechopen.1004802"},{"key":"1565_CR127","first-page":"375","volume-title":"Advances in Pharmacology","author":"R Nag","year":"2025","unstructured":"Nag R, Srivastava S, Rizvi S, Ahmed S, Raza ST (2025) Innovations in vaccine design: Computational tools and techniques. Advances in Pharmacology. Elsevier, pp 375\u2013391"},{"issue":"1","key":"1565_CR128","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1186\/s43141-023-00604-8","volume":"21","author":"M Nahian","year":"2023","unstructured":"Nahian M, Shahab M, Mazumder L, Oliveira JIN, Banu TA, Sarkar MH, Goswami B, Habib A, Begum S, Akter S (2023) In silico design of an epitope-based vaccine against PspC in Streptococcus pneumoniae using reverse vaccinology. J Genet Eng Biotechnol 21(1):166","journal-title":"J Genet Eng Biotechnol"},{"key":"1565_CR129","doi-asserted-by":"crossref","unstructured":"Naveed M, Husnain M, Aziz T, Qadir P, Asim M, Majeed MN, Aloufi AS, Shami A, Alwethynani MS, Tombozara N (2026) Immunoinformatics-based design and evaluation of a multi-epitope vaccine against Vibrio fluvialis. Sci Rep","DOI":"10.1038\/s41598-026-35434-4"},{"issue":"1","key":"1565_CR130","doi-asserted-by":"publisher","first-page":"15587","DOI":"10.1038\/s41598-025-00166-4","volume":"15","author":"M Naveed","year":"2025","unstructured":"Naveed M, Toheed M, Aziz T, Asim M, Qadir P, Rehman HM, Mohamed RAEH, Al-Joufi FA, Alwethaynani MS, Fallatah D (2025) Rational computational design and development of an immunogenic multiepitope vaccine incorporating transmembrane proteins of Fusobacterium necrophorum. Sci Rep 15(1):15587","journal-title":"Sci Rep"},{"issue":"1","key":"1565_CR131","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1186\/s12859-019-2713-9","volume":"20","author":"K Naz","year":"2019","unstructured":"Naz K, Naz A, Ashraf ST, Rizwan M, Ahmad J, Baumbach J, Ali A (2019) PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome. BMC Bioinformatics 20(1):123","journal-title":"BMC Bioinformatics"},{"issue":"W1","key":"1565_CR132","doi-asserted-by":"publisher","first-page":"W36","DOI":"10.1093\/nar\/gkac446","volume":"50","author":"MN Nguyen","year":"2022","unstructured":"Nguyen MN, Krutz NL, Limviphuvadh V, Lopata AL, Gerberick GF, Maurer-Stroh S (2022) AllerCatPro 2.0: a web server for predicting protein allergenicity potential. Nucleic Acids Res 50(W1):W36\u2013W43. https:\/\/doi.org\/10.1093\/nar\/gkac446","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"1565_CR133","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1038\/nbt0608-597b","volume":"26","author":"H Nicholls","year":"2008","unstructured":"Nicholls H (2008) In silico vaccine. Nat Biotechnol 26(6):597\u2013597. https:\/\/doi.org\/10.1038\/nbt0608-597b","journal-title":"Nat Biotechnol"},{"issue":"1","key":"1565_CR134","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s13073-016-0288-x","volume":"8","author":"M Nielsen","year":"2016","unstructured":"Nielsen M, Andreatta M (2016) NetMHCpan-3.0; improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length datasets. Genome Med 8(1):33","journal-title":"Genome Med"},{"key":"1565_CR135","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1016\/j.coi.2017.07.010","volume":"47","author":"DT O\u2019Hagan","year":"2017","unstructured":"O\u2019Hagan DT, Friedland LR, Hanon E, Didierlaurent AM (2017) Towards an evidence based approach for the development of adjuvanted vaccines. Curr Opin Immunol 47:93\u2013102","journal-title":"Curr Opin Immunol"},{"key":"1565_CR136","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/3-540-30791-5_1","volume":"296","author":"MB Oldstone","year":"2005","unstructured":"Oldstone MB (2005) Molecular mimicry, microbial infection, and autoimmune disease: evolution of the concept. Curr Top Microbiol Immunol 296:1\u201317. https:\/\/doi.org\/10.1007\/3-540-30791-5_1","journal-title":"Curr Top Microbiol Immunol"},{"issue":"6","key":"1565_CR137","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1016\/j.drudis.2020.03.006","volume":"25","author":"S Parvizpour","year":"2020","unstructured":"Parvizpour S, Pourseif MM, Razmara J, Rafi MA, Omidi Y (2020) Epitope-based vaccine design: a comprehensive overview of bioinformatics approaches. Drug Discov Today 25(6):1034\u20131042","journal-title":"Drug Discov Today"},{"issue":"24","key":"1565_CR138","doi-asserted-by":"publisher","first-page":"6101","DOI":"10.1007\/s00216-021-03409-1","volume":"413","author":"L Pasquardini","year":"2021","unstructured":"Pasquardini L, Bossi AM (2021) Molecularly imprinted polymers by epitope imprinting: a journey from molecular interactions to the available bioinformatics resources to scout for epitope templates. Anal Bioanal Chem 413(24):6101\u20136115. https:\/\/doi.org\/10.1007\/s00216-021-03409-1","journal-title":"Anal Bioanal Chem"},{"issue":"3","key":"1565_CR139","doi-asserted-by":"publisher","first-page":"844","DOI":"10.1016\/j.jaci.2018.05.021","volume":"143","author":"SU Patil","year":"2019","unstructured":"Patil SU, Shreffler WG (2019) Novel vaccines: Technology and development. J Allergy Clin Immunol 143(3):844\u2013851. https:\/\/doi.org\/10.1016\/j.jaci.2018.05.021","journal-title":"J Allergy Clin Immunol"},{"issue":"1","key":"1565_CR140","doi-asserted-by":"publisher","DOI":"10.3390\/jpm13010116","volume":"13","author":"C Peng","year":"2023","unstructured":"Peng C, Tang F, Wang J, Cheng P, Wang L, Gong W (2023) Immunoinformatic-based multi-epitope vaccine design for co-infection of Mycobacterium tuberculosis and SARS-CoV-2. J Pers Med 13(1):116","journal-title":"J Pers Med"},{"key":"1565_CR141","doi-asserted-by":"crossref","unstructured":"Perez MAS, Cuendet MA, R\u00f6hrig UF, Michielin O, Zoete V (2022) Structural prediction of peptide\u2013MHC binding modes. Computational Peptide Science: Methods and Protocols. 245\u2013282.","DOI":"10.1007\/978-1-0716-1855-4_13"},{"key":"1565_CR142","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1007\/978-1-0716-3239-0_26","volume":"2673","author":"S Piplani","year":"2023","unstructured":"Piplani S, Winkler D, Honda-Okubo Y, Khanna V, Petrovsky N (2023) In silico structure-based vaccine design. Methods Mol Biol 2673:371\u2013399. https:\/\/doi.org\/10.1007\/978-1-0716-3239-0_26","journal-title":"Methods Mol Biol"},{"issue":"12","key":"1565_CR143","doi-asserted-by":"publisher","first-page":"751","DOI":"10.1038\/s41577-022-00707-2","volume":"22","author":"N Pishesha","year":"2022","unstructured":"Pishesha N, Harmand TJ, Ploegh HL (2022) A guide to antigen processing and presentation. Nat Rev Immunol 22(12):751\u2013764","journal-title":"Nat Rev Immunol"},{"issue":"7","key":"1565_CR144","doi-asserted-by":"publisher","first-page":"765","DOI":"10.3390\/biology14070765","volume":"14","author":"P Ponnusamy","year":"2025","unstructured":"Ponnusamy P, Sukumar K, Raja A, Saravanan S, Srinivasan P, Ramya K, Selvaraju M, Saravanan R (2025) Design of a multi-epitope vaccine candidate against infectious laryngotracheitis virus affecting poultry by computational approaches. Biology 14(7):765","journal-title":"Biology"},{"issue":"15","key":"1565_CR145","doi-asserted-by":"publisher","first-page":"1661","DOI":"10.1016\/j.vaccine.2014.01.057","volume":"32","author":"B Di Posteraro","year":"2014","unstructured":"Posteraro B, Pastorino R, Di Giannantonio P, Ianuale C, Amore R, Ricciardi W, Boccia S (2014) The link between genetic variation and variability in vaccine responses: systematic review and meta-analyses. Vaccine 32(15):1661\u20131669. https:\/\/doi.org\/10.1016\/j.vaccine.2014.01.057","journal-title":"Vaccine"},{"key":"1565_CR146","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1016\/B978-0-323-85681-2.00001-X","volume-title":"Brucella Melitensis","author":"JA Pradeepkiran","year":"2021","unstructured":"Pradeepkiran JA, Sainath SB, Balne PK, Bhaskar M (2021) Computational modeling and evaluation of best potential drug targets through comparative modeling. Brucella Melitensis. Elsevier, pp 39\u201378"},{"issue":"3","key":"1565_CR147","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1016\/j.vacun.2024.04.003","volume":"25","author":"P Priyamvada","year":"2024","unstructured":"Priyamvada P, Swetha RG, Dasgupta R, Anbarasu A, Ramaiah S (2024) Immunoinformatics strategy for designing a multi-epitope chimeric vaccine to combat Neisseria gonorrhoeae. Vacunas 25(3):385\u2013402. https:\/\/doi.org\/10.1016\/j.vacun.2024.04.003","journal-title":"Vacunas"},{"issue":"6","key":"1565_CR148","doi-asserted-by":"publisher","first-page":"887","DOI":"10.1007\/s12026-023-09403-2","volume":"71","author":"P Priyamvada","year":"2023","unstructured":"Priyamvada P, Ramaiah S (2023) Pan-genome and reverse vaccinology approaches to design multi-epitope vaccine against Epstein-Barr virus associated with colorectal cancer. Immunol Res 71(6):887\u2013908. https:\/\/doi.org\/10.1007\/s12026-023-09403-2","journal-title":"Immunol Res"},{"issue":"suppl_2","key":"1565_CR149","doi-asserted-by":"publisher","first-page":"W126","DOI":"10.1093\/nar\/gkm219","volume":"35","author":"P Puigbo","year":"2007","unstructured":"Puigbo P, Guzm\u00e1n E, Romeu A, Garcia-Vallv\u00e9 S (2007) OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res 35(suppl_2):W126\u2013W131","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"1565_CR150","doi-asserted-by":"publisher","first-page":"1155","DOI":"10.1007\/s10989-019-09918-z","volume":"26","author":"E Raoufi","year":"2020","unstructured":"Raoufi E, Hemmati M, Eftekhari S, Khaksaran K, Mahmodi Z, Farajollahi MM, Mohsenzadegan M (2020) Epitope prediction by novel immunoinformatics approach: a state-of-the-art review. Int J Pept Res Ther 26(2):1155\u20131163","journal-title":"Int J Pept Res Ther"},{"key":"1565_CR151","doi-asserted-by":"crossref","unstructured":"Rasool D, Jan SA, Khan SU, Nahid N, Ashfaq UA, Umar A, Qasim M, Noor F, Rehman A, Shahzadi K (2024) Subtractive proteomics-based vaccine targets annotation and reverse vaccinology approaches to identify multiepitope vaccine against Plesiomonas shigelloides. Heliyon 10(11)","DOI":"10.1016\/j.heliyon.2024.e31304"},{"issue":"1","key":"1565_CR152","doi-asserted-by":"publisher","first-page":"17626","DOI":"10.1038\/s41598-021-96863-x","volume":"11","author":"K Rawal","year":"2021","unstructured":"Rawal K, Sinha R, Abbasi BA, Chaudhary A, Nath SK, Kumari P, Preeti P, Saraf D, Singh S, Mishra K (2021) Identification of vaccine targets in pathogens and design of a vaccine using computational approaches. Sci Rep 11(1):17626","journal-title":"Sci Rep"},{"issue":"2","key":"1565_CR153","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1093\/sysbio\/syad068","volume":"73","author":"SS Renner","year":"2024","unstructured":"Renner SS, Scherz MD, Schoch CL, Gottschling M, Vences M (2024) Improving the gold standard in NCBI GenBank and related databases: DNA sequences from type specimens and type strains. Syst Biol 73(2):486\u2013494","journal-title":"Syst Biol"},{"key":"1565_CR154","doi-asserted-by":"publisher","first-page":"103992","DOI":"10.1016\/j.meegid.2019.103992","volume":"75","author":"M Rostamtabar","year":"2019","unstructured":"Rostamtabar M, Rahmani A, Baee M, Karkhah A, Prajapati VK, Ebrahimpour S, Nouri HR (2019) Development a multi-epitope driven subunit vaccine for immune response reinforcement against Serogroup B of Neisseria meningitidis using comprehensive immunoinformatics approaches. Infect Genet Evol 75:103992","journal-title":"Infect Genet Evol"},{"issue":"7","key":"1565_CR155","doi-asserted-by":"publisher","DOI":"10.1007\/s13205-024-04022-6","volume":"14","author":"A Roy","year":"2024","unstructured":"Roy A, Swetha RG, Basu S, Biswas R, Ramaiah S, Anbarasu A (2024) Integrating pan-genome and reverse vaccinology to design multi-epitope vaccine against Herpes simplex virus type-1. 3 Biotech 14(7):176. https:\/\/doi.org\/10.1007\/s13205-024-04022-6","journal-title":"3 Biotech"},{"key":"1565_CR156","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbrep.2024.101871","volume":"40","author":"MJ Saadh","year":"2024","unstructured":"Saadh MJ, Ahmed HH, Kareem RA, Baldaniya L, Verma L, Prasad GVS, Chahar M, Taher WM, Alwan M, Jawad MJ, Hamad AK (2024) Design of a novel multi-epitope vaccine candidate against Yersinia pestis using advanced immunoinformatics approaches: an in silico study. Biochem Biophys Rep 40:101871. https:\/\/doi.org\/10.1016\/j.bbrep.2024.101871","journal-title":"Biochem Biophys Rep"},{"key":"1565_CR157","doi-asserted-by":"publisher","DOI":"10.3390\/healthcare11131946","author":"MA Salam","year":"2023","unstructured":"Salam MA, Al-Amin MY, Salam MT, Pawar JS, Akhter N, Rabaan AA, Alqumber MAA (2023) Antimicrobial resistance: a growing serious threat for global public health. Healthcare (Basel). https:\/\/doi.org\/10.3390\/healthcare11131946","journal-title":"Healthcare (Basel)"},{"key":"1565_CR158","doi-asserted-by":"publisher","first-page":"113474","DOI":"10.1016\/j.jim.2023.113474","volume":"517","author":"D Santoni","year":"2023","unstructured":"Santoni D (2023) Peptide Hamming Graphs: A network representation of peptides presented through specific HLAs to identify potential epitope clusters. J Immunol Methods 517:113474","journal-title":"J Immunol Methods"},{"issue":"1","key":"1565_CR159","first-page":"1","volume":"18","author":"RLF Santos","year":"2025","unstructured":"Santos RLF, Melo HCS (2025) GENES HLA E RESPOSTA VACINAL: UMA REVIS\u00c3O NARRATIVA. Rev Multidiscipl N M 18(1):1\u201320","journal-title":"Rev Multidiscipl N M"},{"issue":"3","key":"1565_CR160","doi-asserted-by":"publisher","first-page":"1854","DOI":"10.1021\/acs.jctc.9b01066","volume":"16","author":"S Sasmal","year":"2020","unstructured":"Sasmal S, Gill SC, Lim NM, Mobley DL (2020) Sampling conformational changes of bound ligands using nonequilibrium candidate Monte Carlo and molecular dynamics. J Chem Theory Comput 16(3):1854\u20131865","journal-title":"J Chem Theory Comput"},{"issue":"1","key":"1565_CR161","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.iac.2006.11.005","volume":"27","author":"CH Schein","year":"2007","unstructured":"Schein CH, Ivanciuc O, Braun W (2007) Bioinformatics approaches to classifying allergens and predicting cross-reactivity. Immunol Allergy Clin North Am 27(1):1\u201327","journal-title":"Immunol Allergy Clin North Am"},{"key":"1565_CR162","doi-asserted-by":"crossref","unstructured":"Segala FV, Guido G, Stroffolini G, Masini L, Cattaneo P, Moro L, Motta L, Gobbi F, Nicastri E, Vita S (2025) Insights into the ecological and climate crisis: Emerging infections threatening human health. Acta Trop 262:107531.","DOI":"10.1016\/j.actatropica.2025.107531"},{"issue":"7","key":"1565_CR163","doi-asserted-by":"publisher","first-page":"989","DOI":"10.1128\/CVI.00615-13","volume":"21","author":"YB Seo","year":"2014","unstructured":"Seo YB, Choi WS, Lee J, Song JY, Cheong HJ, Kim WJ (2014) Comparison of the immunogenicity and safety of the conventional subunit, MF59-adjuvanted, and intradermal influenza vaccines in the elderly. Clin Vaccine Immunol 21(7):989\u2013996","journal-title":"Clin Vaccine Immunol"},{"issue":"1","key":"1565_CR164","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-024-66858-5","volume":"14","author":"G Sethi","year":"2024","unstructured":"Sethi G, Varghese RP, Lakra AK, Nayak SS, Krishna R, Hwang JH (2024) Immunoinformatics and structural aided approach to develop multi-epitope based subunit vaccine against Mycobacterium tuberculosis. Sci Rep 14(1):15923. https:\/\/doi.org\/10.1038\/s41598-024-66858-5","journal-title":"Sci Rep"},{"issue":"1","key":"1565_CR165","doi-asserted-by":"publisher","first-page":"15983","DOI":"10.1038\/s41598-022-20397-z","volume":"12","author":"SW Shantier","year":"2022","unstructured":"Shantier SW, Mustafa MI, Abdelmoneim AH, Fadl HA, Elbager SG, Makhawi AM (2022) Novel multi epitope-based vaccine against monkeypox virus: vaccinomic approach. Sci Rep 12(1):15983","journal-title":"Sci Rep"},{"issue":"5","key":"1565_CR166","doi-asserted-by":"publisher","first-page":"bbac174","DOI":"10.1093\/bib\/bbac174","volume":"23","author":"N Sharma","year":"2022","unstructured":"Sharma N, Naorem LD, Jain S, Raghava GPS (2022) ToxinPred2: an improved method for predicting toxicity of proteins. Brief Bioinform 23(5):bbac174","journal-title":"Brief Bioinform"},{"issue":"3","key":"1565_CR167","doi-asserted-by":"publisher","first-page":"954","DOI":"10.1080\/07391102.2021.2015443","volume":"41","author":"S Sharma","year":"2023","unstructured":"Sharma S, Solanki V, Tiwari V (2023) Reverse vaccinology approach to design a vaccine targeting membrane lipoproteins of Salmonella typhi. J Biomol Struct Dyn 41(3):954\u2013969","journal-title":"J Biomol Struct Dyn"},{"key":"1565_CR168","doi-asserted-by":"crossref","unstructured":"Sharma S, Yadav PD, Cherian S (2025) Comprehensive immunoinformatics and bioinformatics strategies for designing a multi-epitope based vaccine targeting structural proteins of Nipah virus. Front Immunol 16:1535322.","DOI":"10.3389\/fimmu.2025.1535322"},{"key":"1565_CR169","doi-asserted-by":"crossref","unstructured":"Shirmohammadpour M, Mirzaei B (2025) Vaccination against pathogenic bacteria: an insight into polysaccharide and conjugate vaccines.","DOI":"10.18502\/jmb.v13i2.18661"},{"key":"1565_CR170","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1007\/978-981-15-6815-2_11","volume-title":"Computer-Aided Drug Design","author":"PS Slathia","year":"2020","unstructured":"Slathia PS, Sharma P (2020) In Silico designing of vaccines: Methods, tools, and their limitations. Computer-Aided Drug Design. Springer, pp 245\u2013277"},{"issue":"1","key":"1565_CR171","doi-asserted-by":"publisher","first-page":"17","DOI":"10.1007\/s10989-022-10486-y","volume":"29","author":"K Srivastava","year":"2023","unstructured":"Srivastava K, Srivastava V (2023) Prediction of conformational and linear B-cell epitopes on envelop protein of zika virus using immunoinformatics approach. Int J Pept Res Ther 29(1):17","journal-title":"Int J Pept Res Ther"},{"issue":"2","key":"1565_CR172","doi-asserted-by":"publisher","first-page":"e1178","DOI":"10.1002\/iid3.1178","volume":"12","author":"BA Suliman","year":"2024","unstructured":"Suliman BA (2024) Potential clinical implications of molecular mimicry-induced autoimmunity. Immun Inflamm Dis 12(2):e1178. https:\/\/doi.org\/10.1002\/iid3.1178","journal-title":"Immun Inflamm Dis"},{"key":"1565_CR173","doi-asserted-by":"publisher","DOI":"10.3389\/fonc.2025.1592072","volume":"15","author":"P Sun","year":"2025","unstructured":"Sun P, Wang L, Liu Z, Xu Z (2025) Design and immunogenic evaluation of multi-epitope vaccines for colorectal cancer: insights from molecular dynamics and in-vitro studies. Front Oncol 15:1592072","journal-title":"Front Oncol"},{"key":"1565_CR174","doi-asserted-by":"crossref","unstructured":"Sunita, Sajid A, Singh Y, Shukla P (2020b) Computational tools for modern vaccine development. Hum Vaccin Immunother 16(3):723\u2013735.","DOI":"10.1080\/21645515.2019.1670035"},{"key":"1565_CR175","doi-asserted-by":"publisher","unstructured":"Sunita, Sajid A, Singh Y, Shukla P (2020a) Computational tools for modern vaccine development. Hum Vaccin Immunother 16(3):723\u2013735 https:\/\/doi.org\/10.1080\/21645515.2019.1670035","DOI":"10.1080\/21645515.2019.1670035"},{"key":"1565_CR176","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/j.jtbi.2016.04.009","volume":"400","author":"RG Swetha","year":"2016","unstructured":"Swetha RG, Sandhya M, Ramaiah S, Anbarasu A (2016) Identification of CD4+ T-cell epitope and investigation of HLA distribution for the immunogenic proteins of Burkholderia pseudomallei using in silico approaches \u2013 A key vaccine development strategy for melioidosis. J Theor Biol 400:11\u201318. https:\/\/doi.org\/10.1016\/j.jtbi.2016.04.009","journal-title":"J Theor Biol"},{"issue":"11","key":"1565_CR177","doi-asserted-by":"publisher","first-page":"2504","DOI":"10.3390\/v14112504","volume":"14","author":"RG Swetha","year":"2022","unstructured":"Swetha RG, Basu S, Ramaiah S, Anbarasu A (2022) Multi-epitope vaccine for monkeypox using pan-genome and reverse vaccinology approaches. Viruses 14(11):2504","journal-title":"Viruses"},{"issue":"2","key":"1565_CR178","doi-asserted-by":"publisher","first-page":"191","DOI":"10.4103\/ijmy.ijmy_70_25","volume":"14","author":"SC Theorupun","year":"2025","unstructured":"Theorupun SC, Massi MN, Nurhasanah A, Syamsuri F, Hatta M, Rasita YD, Hidayah N, Karimah N, Utomo DIS (2025) PPE18 and PepA variations in Mycobacterium tuberculosis clinical isolates from Makassar, Indonesia: challenges for immune recognition and vaccine development. Int J Mycobacteriol 14(2):191\u2013200","journal-title":"Int J Mycobacteriol"},{"key":"1565_CR179","doi-asserted-by":"publisher","first-page":"115865","DOI":"10.1016\/j.bmc.2020.115865","volume":"29","author":"A Thorarensen","year":"2021","unstructured":"Thorarensen A, Balbo P, Banker ME, Czerwinski RM, Kuhn M, Maurer TS, Telliez JB, Vincent F, Wittwer AJ (2021) The advantages of describing covalent inhibitor in vitro potencies by IC50 at a fixed time point. IC50 determination of covalent inhibitors provides meaningful data to medicinal chemistry for SAR optimization. Bioorg Med Chem 29:115865","journal-title":"Bioorg Med Chem"},{"issue":"4","key":"1565_CR180","doi-asserted-by":"publisher","first-page":"bbac259","DOI":"10.1093\/bib\/bbac259","volume":"23","author":"R Trevizani","year":"2022","unstructured":"Trevizani R, Yan Z, Greenbaum JA, Sette A, Nielsen M, Peters B (2022) A comprehensive analysis of the IEDB MHC class-I automated benchmark. Brief Bioinform 23(4):bbac259","journal-title":"Brief Bioinform"},{"issue":"19","key":"1565_CR181","doi-asserted-by":"publisher","first-page":"4852","DOI":"10.3390\/cancers13194852","volume":"13","author":"GR Tundo Jr","year":"2021","unstructured":"Tundo GR, Sbardella D, Oddone F, Kudriaeva AA, Lacal PM, Belogurov AA Jr, Graziani G, Marini S (2021) At the cutting edge against cancer: a perspective on immunoproteasome and immune checkpoints modulation as a potential therapeutic intervention. Cancers 13(19):4852","journal-title":"Cancers"},{"issue":"8","key":"1565_CR182","doi-asserted-by":"publisher","first-page":"942","DOI":"10.1093\/bioinformatics\/btm061","volume":"23","author":"C-W Tung","year":"2007","unstructured":"Tung C-W, Ho S-Y (2007) POPI: predicting immunogenicity of MHC class I binding peptides by mining informative physicochemical properties. Bioinformatics 23(8):942\u2013949","journal-title":"Bioinformatics"},{"issue":"6","key":"1565_CR183","doi-asserted-by":"publisher","first-page":"577","DOI":"10.3390\/vetsci12060577","volume":"12","author":"S Ullah","year":"2025","unstructured":"Ullah S, Ullah H, Fatima K, Lei T (2025) In silico designed multi-epitope vaccine based on the conserved fragments in viral proteins for broad-spectrum protection against porcine reproductive and respiratory syndrome virus. Vet Sci 12(6):577","journal-title":"Vet Sci"},{"issue":"5","key":"1565_CR184","doi-asserted-by":"publisher","first-page":"731","DOI":"10.37349\/ei.2022.00079","volume":"2","author":"VN Uversky","year":"2022","unstructured":"Uversky VN (2022) Fight fire with fire: the need for a vaccine based on intrinsic disorder and structural flexibility. Exploration of Immunology 2(5):731\u2013748. https:\/\/doi.org\/10.37349\/ei.2022.00079","journal-title":"Exploration of Immunology"},{"issue":"21","key":"1565_CR185","doi-asserted-by":"publisher","first-page":"3036","DOI":"10.1002\/cbic.202000261","volume":"21","author":"A De Uvyn","year":"2020","unstructured":"Uvyn A, De Geest BG (2020) Multivalent antibody-recruiting macromolecules: linking increased binding affinity with enhanced innate immune killing. ChemBioChem 21(21):3036\u20133043","journal-title":"ChemBioChem"},{"key":"1565_CR186","doi-asserted-by":"publisher","DOI":"10.3390\/biomedicines10092126","author":"F Vacca","year":"2022","unstructured":"Vacca F, Sala C, Rappuoli R (2022) Monoclonal antibodies for bacterial pathogens: mechanisms of action and engineering approaches for enhanced effector functions. Biomedicines. https:\/\/doi.org\/10.3390\/biomedicines10092126","journal-title":"Biomedicines"},{"issue":"2","key":"1565_CR187","doi-asserted-by":"publisher","first-page":"12","DOI":"10.3390\/vaccines4020012","volume":"4","author":"A Vartak","year":"2016","unstructured":"Vartak A, Sucheck SJ (2016) Recent advances in subunit vaccine carriers. Vaccines 4(2):12","journal-title":"Vaccines"},{"key":"1565_CR188","doi-asserted-by":"crossref","unstructured":"Velankar S, Burley SK, Kurisu G, Hoch JC, Markley JL (2021) The Protein Data Bank archive. In: Owens RJ (ed) Structural proteomics: high-throughput methods. Methods in molecular biology, vol 2305. Humana, New York, pp 3\u201321.","DOI":"10.1007\/978-1-0716-1406-8_1"},{"key":"1565_CR189","doi-asserted-by":"publisher","first-page":"1159798","DOI":"10.3389\/fcimb.2023.1159798","volume":"13","author":"P Venkateswaran","year":"2023","unstructured":"Venkateswaran P, Vasudevan S, David H, Shaktivel A, Shanmugam K, Neelakantan P, Solomon AP (2023) Revisiting ESKAPE pathogens: virulence, resistance, and combating strategies focusing on quorum sensing. Front Cell Infect Microbiol 13:1159798. https:\/\/doi.org\/10.3389\/fcimb.2023.1159798","journal-title":"Front Cell Infect Microbiol"},{"issue":"1","key":"1565_CR190","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1002\/prot.26188","volume":"90","author":"J Verburgt","year":"2022","unstructured":"Verburgt J, Kihara D (2022) Benchmarking of structure refinement methods for protein complex models. Proteins 90(1):83\u201395","journal-title":"Proteins"},{"issue":"D1","key":"1565_CR191","doi-asserted-by":"publisher","first-page":"D339","DOI":"10.1093\/nar\/gkae1092","volume":"47","author":"R Vita","year":"2018","unstructured":"Vita R, Blazeska N, Marrama D, Duesing S, Bennett J, Greenbaum J, De Almeida Mendes M, Mahita J, Wheeler DK, Cantrell JR, Overton JA, Natale DA, Sette A, Peters B (2025) The Immune Epitope Database (IEDB): 2024 update. Nucleic Acids Res 53(D1):D436\u2013D443 https:\/\/doi.org\/10.1093\/nar\/gkae1092","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"1565_CR192","doi-asserted-by":"publisher","first-page":"D339","DOI":"10.1093\/nar\/gky1006","volume":"47","author":"R Vita","year":"2018","unstructured":"Vita R, Mahajan S, Overton JA, Dhanda SK, Martini S, Cantrell JR, Wheeler DK, Sette A, Peters B (2018) The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res 47(D1):D339\u2013D343. https:\/\/doi.org\/10.1093\/nar\/gky1006","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"1565_CR193","doi-asserted-by":"publisher","first-page":"100042","DOI":"10.1016\/j.gmg.2025.100042","volume":"12","author":"KE Vivekanandan","year":"2025","unstructured":"Vivekanandan KE, Kumar PV, Jaysree RC, Rajeshwari T (2025) Exploring molecular mechanisms of drug resistance in bacteria and progressions in CRISPR\/Cas9-based genome expurgation solutions. Glob Med Genet 12(2):100042. https:\/\/doi.org\/10.1016\/j.gmg.2025.100042","journal-title":"Glob Med Genet"},{"issue":"29","key":"1565_CR194","doi-asserted-by":"publisher","first-page":"32116","DOI":"10.1021\/acsomega.4c04246","volume":"9","author":"J-H Wang","year":"2024","unstructured":"Wang J-H, Sung T-Y (2024) ToxTeller: predicting peptide toxicity using four different machine learning approaches. ACS Omega 9(29):32116\u201332123. https:\/\/doi.org\/10.1021\/acsomega.4c04246","journal-title":"ACS Omega"},{"key":"1565_CR195","doi-asserted-by":"crossref","unstructured":"Wang M, Kurgan L, Li M (2023) A comprehensive assessment and comparison of tools for HLA class I peptide-binding prediction. Brief Bioinform 24(3):bbad150.","DOI":"10.1093\/bib\/bbad150"},{"issue":"1","key":"1565_CR196","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1186\/s13104-021-05531-w","volume":"14","author":"G Xie","year":"2021","unstructured":"Xie G, Fair JM (2021) Hidden Markov Model: a shortest unique representative approach to detect the protein toxins, virulence factors and antibiotic resistance genes. BMC Res Notes 14(1):122","journal-title":"BMC Res Notes"},{"key":"1565_CR197","doi-asserted-by":"publisher","DOI":"10.1016\/j.lddd.2025.100222","author":"Y Xin","year":"2026","unstructured":"Xin Y, Chang W, Wang Q (2026) Investigating the mechanism of luteolin in the treatment of inflammatory bowel disease based on network pharmacology, normal mode analysis and experimental validation. Lett Drug Des Discov. https:\/\/doi.org\/10.1016\/j.lddd.2025.100222","journal-title":"Lett Drug Des Discov"},{"key":"1565_CR198","doi-asserted-by":"crossref","unstructured":"Yang Y, Wei Z, Cia G, Song X, Pucci F, Rooman M, Xue F, Hou Q (2024) MHCII-peptide presentation: an assessment of the state-of-the-art prediction methods. Front Immunol 15:1293706.","DOI":"10.3389\/fimmu.2024.1293706"},{"issue":"1","key":"1565_CR199","doi-asserted-by":"publisher","first-page":"e29404","DOI":"10.2196\/29404","volume":"3","author":"C Ye","year":"2022","unstructured":"Ye C, Hu W, Gaeta B (2022) Prediction of antibody-antigen binding via machine learning: development of data sets and evaluation of methods. JMIR Bioinform Biotech 3(1):e29404","journal-title":"JMIR Bioinform Biotech"},{"issue":"1","key":"1565_CR200","doi-asserted-by":"publisher","first-page":"e013271","DOI":"10.1136\/jitc-2025-013271","volume":"14","author":"BKQ Zaghla","year":"2026","unstructured":"Zaghla BKQ, Safy\u00fcrek Z, Gr\u00f6ger D, Mecklenbr\u00e4uker S, Lingst\u00e4dt NS, Popp O, Spengler J, Haji M, Montesion M, Albacker LA, Mertins P, Klatt MG (2026) Systematic evaluation of neoepitope predictions challenges clinically observed T-cell responses and their impact on immune evasion. J Immunother Cancer 14(1):e013271. https:\/\/doi.org\/10.1136\/jitc-2025-013271","journal-title":"J Immunother Cancer"},{"key":"1565_CR201","doi-asserted-by":"crossref","unstructured":"Zaru R, Orchard S, UniProt Consortium (2023) UniProt tools: BLAST, align, peptide search, and ID mapping. Curr Protoc 3(3):e697.","DOI":"10.1002\/cpz1.697"},{"key":"1565_CR202","doi-asserted-by":"crossref","unstructured":"Zhang J, Tao A (2015) Antigenicity, Immunogenicity, Allergenicity: Allergy Bioinformatics. 2015 Nov 3;8:175\u2009\u2212\u200986. doi: 10.1007\/978-94-017-7444-4_11. eCollection 2015.","DOI":"10.1007\/978-94-017-7444-4_11"},{"issue":"2","key":"1565_CR203","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1038\/cmi.2017.92","volume":"15","author":"L Zhang","year":"2018","unstructured":"Zhang L (2018) Multi-epitope vaccines: a promising strategy against tumors and viral infections. Cell Mol Immunol 15(2):182\u2013184. https:\/\/doi.org\/10.1038\/cmi.2017.92","journal-title":"Cell Mol Immunol"},{"key":"1565_CR204","doi-asserted-by":"crossref","unstructured":"Zhang MQ, Bu JW, Wang ZG, Liu SL (2025) The design and prospects of influenza virus vaccines based on conserved epitopes and adjuvant optimization. Vaccines 3(2):16.","DOI":"10.3390\/targets3020016"},{"issue":"suppl_2","key":"1565_CR205","doi-asserted-by":"publisher","first-page":"W513","DOI":"10.1093\/nar\/gkn254","volume":"36","author":"Q Zhang","year":"2008","unstructured":"Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui H-H, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B (2008) Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res 36(suppl_2):W513\u2013W518. https:\/\/doi.org\/10.1093\/nar\/gkn254","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1565_CR206","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1038\/s41392-023-01557-7","volume":"8","author":"T Zhao","year":"2023","unstructured":"Zhao T, Cai Y, Jiang Y, He X, Wei Y, Yu Y, Tian X (2023) Vaccine adjuvants: mechanisms and platforms. Signal Transduct Target Ther 8(1):283. https:\/\/doi.org\/10.1038\/s41392-023-01557-7","journal-title":"Signal Transduct Target Ther"},{"issue":"1","key":"1565_CR207","doi-asserted-by":"publisher","first-page":"10425","DOI":"10.1038\/s41598-025-90226-6","volume":"15","author":"F Zhu","year":"2025","unstructured":"Zhu F, Qin R, Ma S, Zhou Z, Tan C, Yang H, Zhang P, Xu Y, Luo Y, Chen J, Pan P (2025) Designing a multi-epitope vaccine against Pseudomonas aeruginosa via integrating reverse vaccinology with immunoinformatics approaches. Sci Rep 15(1):10425. https:\/\/doi.org\/10.1038\/s41598-025-90226-6","journal-title":"Sci Rep"},{"key":"1565_CR208","doi-asserted-by":"publisher","first-page":"1730217","DOI":"10.3389\/fimmu.2026.1730217","volume":"17","author":"J Zum\u00e1rraga","year":"2026","unstructured":"Zum\u00e1rraga J, L\u00f3pez D, Sotillo J, McConnell MJ, Mart\u00edn-Galiano AJ (2026) Is the reverse vaccinology idea becoming exhausted? Front Immunol 17:1730217. https:\/\/doi.org\/10.3389\/fimmu.2026.1730217","journal-title":"Front Immunol"}],"container-title":["Folia Microbiologica"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s12223-026-01565-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s12223-026-01565-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s12223-026-01565-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,1]],"date-time":"2026-08-01T06:03:09Z","timestamp":1785564189000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s12223-026-01565-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,1]]},"references-count":208,"alternative-id":["1565"],"URL":"https:\/\/doi.org\/10.1007\/s12223-026-01565-4","relation":{},"ISSN":["0015-5632","1874-9356"],"issn-type":[{"value":"0015-5632","type":"print"},{"value":"1874-9356","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,1]]},"assertion":[{"value":"10 May 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 July 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 August 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","label":"Competing interest","group":{"name":"EthicsHeading","label":"Declarations"}}]}}