{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T19:06:24Z","timestamp":1783969584445,"version":"3.55.0"},"reference-count":94,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2025,7,8]],"date-time":"2025-07-08T00:00:00Z","timestamp":1751932800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>Recent outbreaks caused by hMPXV, especially hMPXV lineages\/sub-lineages, represent public health threats necessitating stringent prophylactic measures to ameliorate their colossal impact. The current study annotated the EEV form of hMPXV\u2019s target proteins to formulate a reverse vaccinology-dependent hMPXV multiepitope vaccine. Epitope determination, followed by vaccine formulation, was undertaken. The promising formulation was validated for its potential to trigger immune responses immunoinformatically. The MPXV-1-Beta formulation was characterised as a promising candidate based on antigenicity score, physicochemical properties, solubility score, ProSA Z-score, and Ramachandran plot. Docking, normal mode analysis, and molecular dynamic simulation of MPXV-1-Beta with TLRs and MHCs authenticated rigid docking and its efficacy in enhancing immune receptor activation under physiological conditions. MPXV-1-Beta was discerned to trigger a sustained immune response (IR) with a broader average population coverage of 97.526, SD = 12.44. The proposed MPXV-1-Beta candidate showed significant potential. The findings of this study provide a preliminary framework for developing an efficacious hMPXV vaccine; however, extensive in vitro, in vivo, and clinical evaluations are required to substantiate the computational insights.<\/jats:p>","DOI":"10.3390\/biology14070830","type":"journal-article","created":{"date-parts":[[2025,7,8]],"date-time":"2025-07-08T09:12:48Z","timestamp":1751965968000},"page":"830","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Annotation of the Extracellular Enveloped Form of Monkeypox Virus for the Design, Screening, Validation, and Simulation of a Chimeric Vaccine Construct"],"prefix":"10.3390","volume":"14","author":[{"given":"Mohammad Asrar","family":"Izhari","sequence":"first","affiliation":[{"name":"Faculty of Applied Medical Sciences, Al-Baha University, Al Baha 65522, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Essa Ajmi","family":"Alodeani","sequence":"additional","affiliation":[{"name":"Department of Dermatology, Al-Kharj Military Hospital, Al-Kharj 11361, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Siraj B.","family":"Alharthi","sequence":"additional","affiliation":[{"name":"Molecular Genetics Unit, Alhada Armed Forces Hospital, Taif 26792, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmad H. A.","family":"Almontasheri","sequence":"additional","affiliation":[{"name":"Ibn Sina Hospital for Extended Care, Makka 24247, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Foton E.","family":"Alotaibi","sequence":"additional","affiliation":[{"name":"Genetic Counselling Department National Guard Hospital Riyadh, Riyadh 11426, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rakan E.","family":"Alotaibi","sequence":"additional","affiliation":[{"name":"College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wael A.","family":"Alghamdi","sequence":"additional","affiliation":[{"name":"Laboratory Department, King Faha Hospital, Al-Bhaha 65732, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Osama","family":"Abdulaziz","sequence":"additional","affiliation":[{"name":"Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-4724-5337","authenticated-orcid":false,"given":"Fahad","family":"Alghamdi","sequence":"additional","affiliation":[{"name":"Prince Mishari Bin Saud Hospital, Baljurshi 65639, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali","family":"Alisaac","sequence":"additional","affiliation":[{"name":"Faculty of Applied Medical Sciences, Al-Baha University, Al Baha 65522, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mansoor","family":"Alsahag","sequence":"additional","affiliation":[{"name":"Faculty of Applied Medical Sciences, Al-Baha University, Al Baha 65522, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed R. 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Med., 12.","DOI":"10.3390\/jcm12030914"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1056\/NEJMoa2207323","article-title":"Monkeypox virus infection in humans across 16 countries\u2014April\u2013June 2022","volume":"387","author":"Thornhill","year":"2022","journal-title":"N. Engl. J. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"e554","DOI":"10.1016\/S2666-5247(22)00153-7","article-title":"Global human monkeypox outbreak: Atypical presentation demanding urgent public health action","volume":"3","author":"Otu","year":"2022","journal-title":"Lancet Microbe"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"17","DOI":"10.2217\/17460913.2.1.17","article-title":"Human monkeypox: An emerging zoonotic disease","volume":"2","author":"Parker","year":"2007","journal-title":"Future Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1093\/cid\/cit703","article-title":"Human monkeypox","volume":"58","author":"McCollum","year":"2014","journal-title":"Clin. Infect. Dis."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1128\/br.37.1.1-18.1973","article-title":"Monkeypox virus","volume":"37","author":"Cho","year":"1973","journal-title":"Bacteriol. Rev."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1016\/j.jiph.2023.01.011","article-title":"The recent re-emergence of human monkeypox: Would it become endemic beyond Africa?","volume":"16","author":"Hakim","year":"2023","journal-title":"J. Infect. Public Health"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"104069","DOI":"10.1016\/j.amsu.2022.104069","article-title":"The outbreak of monkeypox 2022: An overview","volume":"79","author":"Hraib","year":"2022","journal-title":"Ann. Med. Surg."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1408","DOI":"10.1038\/s41564-024-01690-1","article-title":"Understanding the biology of monkeypox virus to prevent future outbreaks","volume":"9","author":"Moss","year":"2024","journal-title":"Nat. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"198932","DOI":"10.1016\/j.virusres.2022.198932","article-title":"The virology of human monkeypox virus (hMPXV): A brief overview","volume":"322","author":"Lansiaux","year":"2022","journal-title":"Virus Res."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"3285","DOI":"10.1111\/all.16374","article-title":"Monkeypox 2024 outbreak: Fifty essential questions and answers","volume":"79","author":"Cabanillas","year":"2024","journal-title":"Allergy"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1652","DOI":"10.1001\/jama.2024.21091","article-title":"Mpox clinical presentation, diagnostic approaches, and treatment strategies: A review","volume":"332","author":"Titanji","year":"2024","journal-title":"JAMA"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"257","DOI":"10.15585\/mmwr.mm6510a2","article-title":"Use of vaccinia virus smallpox vaccine in laboratory and health care personnel at risk for occupational exposure to orthopoxviruses\u2014Recommendations of the Advisory Committee on Immunization Practices (ACIP), 2015","volume":"65","author":"Petersen","year":"2016","journal-title":"MMWR. Morb. Mortal. Wkly. Rep."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"734","DOI":"10.15585\/mmwr.mm7122e1","article-title":"Use of JYNNEOS (smallpox and monkeypox vaccine, live, nonreplicating) for preexposure vaccination of persons at risk for occupational exposure to orthopoxviruses: Recommendations of the Advisory Committee on Immunization Practices\u2014United States, 2022","volume":"71","author":"Rao","year":"2022","journal-title":"MMWR. Morb. Mortal. Wkly. Rep."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.tim.2011.12.001","article-title":"Outbreaks of human monkeypox after cessation of smallpox vaccination","volume":"20","author":"Reynolds","year":"2012","journal-title":"Trends Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1038\/s41577-022-00775-4","article-title":"Monkeypox: Disease epidemiology, host immunity and clinical interventions","volume":"22","author":"Lum","year":"2022","journal-title":"Nat. Rev. Immunol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"5948","DOI":"10.1038\/s41467-023-41587-x","article-title":"Monkeypox virus-infected individuals mount comparable humoral immune responses as Smallpox-vaccinated individuals","volume":"14","author":"Otter","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"71","DOI":"10.2147\/DDDT.S3687","article-title":"ACAM2000\u2122: The new smallpox vaccine for United States Strategic National Stockpile","volume":"25","author":"Nalca","year":"2010","journal-title":"Drug Des. Dev. Ther."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Shi, D., He, P., Song, Y., Cheng, S., Linhardt, R.J., Dordick, J.S., Chi, L., and Zhang, F. (2022). Kinetic and structural aspects of glycosaminoglycan\u2013monkeypox virus protein A29 interactions using surface plasmon resonance. Molecules, 27.","DOI":"10.3390\/molecules27185898"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1016\/j.virs.2022.07.006","article-title":"Monkeypox virus: A re-emergent threat to humans","volume":"37","author":"Gong","year":"2022","journal-title":"Virol. Sin."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1006\/viro.2002.1446","article-title":"Analysis of the monkeypox virus genome","volume":"297","author":"Shchelkunov","year":"2002","journal-title":"Virology"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"4192","DOI":"10.1128\/JVI.72.5.4192-4204.1998","article-title":"The envelope protein encoded by the A33R gene is required for formation of actin-containing microvilli and efficient cell-to-cell spread of vaccinia virus","volume":"72","author":"Roper","year":"1998","journal-title":"J. Virol."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Sagdat, K., Batyrkhan, A., and Kanayeva, D. (2024). Exploring monkeypox virus proteins and rapid detection techniques. Front. Cell. Infect. Microbiol., 14.","DOI":"10.3389\/fcimb.2024.1414224"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1038\/s41422-023-00792-5","article-title":"Polyvalent mRNA vaccination elicited potent immune response to monkeypox virus surface antigens","volume":"33","author":"Fang","year":"2023","journal-title":"Cell Res."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"5209","DOI":"10.1002\/jmv.27017","article-title":"Bioinformatics and immunoinformatics to support COVID-19 vaccine development","volume":"93","author":"Ishack","year":"2021","journal-title":"J. Med. Virol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"D678","DOI":"10.1093\/nar\/gkac1003","article-title":"Introducing the bacterial and viral bioinformatics resource center (BV-BRC): A resource combining PATRIC, IRD and ViPR","volume":"51","author":"Olson","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"D204","DOI":"10.1093\/nar\/gku989","article-title":"UniProt: A hub for protein information","volume":"43","author":"Consortium","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"680","DOI":"10.1093\/bioinformatics\/btq003","article-title":"CD-HIT Suite: A web server for clustering and comparing biological sequences","volume":"26","author":"Huang","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1002\/prot.21078","article-title":"Prediction of continuous B-cell epitopes in an antigen using recurrent neural network","volume":"65","author":"Saha","year":"2006","journal-title":"Proteins Struct. Funct. Bioinform."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Fleri, W., Paul, S., Dhanda, S.K., Mahajan, S., Xu, X., Peters, B., and Sette, A. (2017). The immune epitope database and analysis resource in epitope discovery and synthetic vaccine design. Front. Immunol., 8.","DOI":"10.3389\/fimmu.2017.00278"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Dhanda, S.K., Vir, P., and Raghava, G.P. (2013). Designing of interferon-gamma inducing MHC class-II binders. Biol. Direct., 8.","DOI":"10.1186\/1745-6150-8-30"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"263952","DOI":"10.1155\/2013\/263952","article-title":"Prediction of IL4 inducing peptides","volume":"2013","author":"Dhanda","year":"2013","journal-title":"Clin. Dev. Immunol."},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Doytchinova, I.A., and Flower, D.R. (2007). VaxiJen: A server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinform., 8.","DOI":"10.1186\/1471-2105-8-4"},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Gupta, S., Kapoor, P., Chaudhary, K., Gautam, A., Kumar, R., Consortium, O.S.D.D., and Raghava, G.P. (2013). In silico approach for predicting toxicity of peptides and proteins. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0073957"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1093\/bioinformatics\/btaa1102","article-title":"SoluProt: Prediction of soluble protein expression in Escherichia coli","volume":"37","author":"Hon","year":"2021","journal-title":"Bioinformatics"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Dimitrov, I., Flower, D.R., and Doytchinova, I. (2013). AllerTOP\u2014A server for in silico prediction of allergens. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-S6-S4"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Fadaka, A.O., Sibuyi, N.R.S., Martin, D.R., Goboza, M., Klein, A., Madiehe, A.M., and Meyer, M. (2021). Immunoinformatics design of a novel epitope-based vaccine candidate against dengue virus. Sci. Rep., 11.","DOI":"10.1038\/s41598-021-99227-7"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/0092-8674(86)90762-2","article-title":"Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes","volume":"44","author":"Kozak","year":"1986","journal-title":"Cell"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.biosystems.2005.05.005","article-title":"Comparative analysis of base biases around the stop codons in six eukaryotes","volume":"81","author":"Liu","year":"2005","journal-title":"Biosystems"},{"key":"ref_42","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."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"309","DOI":"10.4049\/jimmunol.180.1.309","article-title":"Increased antigen presentation efficiency by coupling antigens to MHC class I trafficking signals","volume":"180","author":"Kreiter","year":"2008","journal-title":"J. Immunol."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"2108","DOI":"10.1101\/gad.5.11.2108","article-title":"The cap and poly (A) tail function synergistically to regulate mRNA translational efficiency","volume":"5","author":"Gallie","year":"1991","journal-title":"Genes Dev."},{"key":"ref_45","first-page":"3441","article-title":"mRNA poly (A) tail, a 3\u2032 enhancer of translational initiation","volume":"10","author":"Munroe","year":"1990","journal-title":"Mol. Cell. Biol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1016\/0968-0004(89)90011-X","article-title":"Poly (A), poly (A) binding protein and the regulation of mRNA stability","volume":"14","author":"Bernstein","year":"1989","journal-title":"Trends Biochem. Sci."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"9053","DOI":"10.1158\/0008-5472.CAN-10-2880","article-title":"Multiple injections of electroporated autologous T cells expressing a chimeric antigen receptor mediate regression of human disseminated tumor","volume":"70","author":"Zhao","year":"2010","journal-title":"Cancer Res."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"4009","DOI":"10.1182\/blood-2006-04-015024","article-title":"Modification of antigen-encoding RNA increases stability, translational efficacy, and T-cell stimulatory capacity of dendritic cells","volume":"108","author":"Holtkamp","year":"2006","journal-title":"Blood"},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Pourseif, M.M., Parvizpour, S., Jafari, B., Dehghani, J., Naghili, B., and Omidi, Y. (2020). A domain-based vaccine construct against SARS-CoV-2, the causative agent of COVID-19 pandemic: Development of self-amplifying mRNA and peptide vaccines. BioImpacts BI, 11.","DOI":"10.21203\/rs.3.rs-32539\/v1"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"4552","DOI":"10.1128\/MCB.19.7.4552","article-title":"An mRNA stability complex functions with poly (A)-binding protein to stabilize mRNA in vitro","volume":"19","author":"Wang","year":"1999","journal-title":"Mol. Cell. Biol."},{"key":"ref_51","first-page":"06","article-title":"In silico structural delineation of nucleocapsid protein of SARS-CoV-2","volume":"8","author":"Priyadarsini","year":"2020","journal-title":"J. Entomol. Zool. Stud."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"W402","DOI":"10.1093\/nar\/gkz297","article-title":"The PSIPRED protein analysis workbench: 20 years on","volume":"47","author":"Buchan","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"W70","DOI":"10.1093\/nar\/gkn188","article-title":"The vienna RNA websuite","volume":"36","author":"Gruber","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1748-7188-6-26","article-title":"ViennaRNA Package 2.0","volume":"6","author":"Lorenz","year":"2011","journal-title":"Algorithms Mol. Biol."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"W526","DOI":"10.1093\/nar\/gkh468","article-title":"Protein structure prediction and analysis using the Robetta server","volume":"32","author":"Kim","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"W384","DOI":"10.1093\/nar\/gkt458","article-title":"GalaxyRefine: Protein structure refinement driven by side-chain repacking","volume":"41","author":"Heo","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"W407","DOI":"10.1093\/nar\/gkm290","article-title":"ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins","volume":"35","author":"Wiederstein","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/nprot.2016.169","article-title":"The ClusPro web server for protein\u2013protein docking","volume":"12","author":"Kozakov","year":"2017","journal-title":"Nat. Protoc."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1002\/pro.3289","article-title":"PDBsum: Structural summaries of PDB entries","volume":"27","author":"Laskowski","year":"2018","journal-title":"Protein Sci."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"W271","DOI":"10.1093\/nar\/gku339","article-title":"iMODS: Internal coordinates normal mode analysis server","volume":"42","author":"Aliaga","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1691","DOI":"10.1021\/acs.jcim.2c00044","article-title":"GROMACS in the cloud: A global supercomputer to speed up alchemical drug design","volume":"62","author":"Kutzner","year":"2022","journal-title":"J. Chem. Inf. Model."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"W526","DOI":"10.1093\/nar\/gki376","article-title":"JCat: A novel tool to adapt codon usage of a target gene to its potential expression host","volume":"33","author":"Grote","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_63","doi-asserted-by":"crossref","unstructured":"Fu, H., Liang, Y., Zhong, X., Pan, Z., Huang, L., Zhang, H., Xu, Y., Zhou, W., and Liu, Z. (2020). Codon optimization with deep learning to enhance protein expression. Sci. Rep., 10.","DOI":"10.1038\/s41598-020-74091-z"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"1617","DOI":"10.1080\/07391102.2021.2024253","article-title":"Modeling mRNA-based vaccine YFV. E1988 against yellow fever virus E-protein using immuno-informatics and reverse vaccinology approach","volume":"41","author":"Khan","year":"2023","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Rapin, N., Lund, O., Bernaschi, M., and Castiglione, F. (2010). Computational immunology meets bioinformatics: The use of prediction tools for molecular binding in the simulation of the immune system. PLoS ONE, 5.","DOI":"10.1371\/journal.pone.0009862"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Bui, H.-H., Sidney, J., Dinh, K., Southwood, S., Newman, M.J., and Sette, A. (2006). Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinform., 7.","DOI":"10.1186\/1471-2105-7-153"},{"key":"ref_67","first-page":"593","article-title":"A human infection caused by monkeypox virus in Basankusu Territory, Democratic Republic of the Congo","volume":"46","author":"Ladnyj","year":"1972","journal-title":"Bull. World Health Organ."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.bj.2020.09.005","article-title":"Development of multi-epitope peptide-based vaccines against SARS-CoV-2","volume":"44","author":"Lim","year":"2021","journal-title":"Biomed. J."},{"key":"ref_69","doi-asserted-by":"crossref","unstructured":"Yang, Z., Bogdan, P., and Nazarian, S. (2021). An in silico deep learning approach to multi-epitope vaccine design: A SARS-CoV-2 case study. Sci. Rep., 11.","DOI":"10.1038\/s41598-021-81749-9"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"110804","DOI":"10.1016\/j.humimm.2024.110804","article-title":"Multi-epitope vaccines, from design to expression; an in silico approach","volume":"85","author":"Mortazavi","year":"2024","journal-title":"Hum. Immunol."},{"key":"ref_71","doi-asserted-by":"crossref","unstructured":"Yin, D., Li, L., Song, X., Li, H., Wang, J., Ju, W., Qu, X., Song, D., Liu, Y., and Meng, X. (2016). A novel multi-epitope recombined protein for diagnosis of human brucellosis. BMC Infect. Dis., 16.","DOI":"10.1186\/s12879-016-1552-9"},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Bui, H.H., Sidney, J., Li, W., Fusseder, N., and Sette, A. (2007). Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinform., 8.","DOI":"10.1186\/1471-2105-8-361"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1016\/j.bj.2016.11.004","article-title":"In silico structure analysis and epitope prediction of E3 CR1-beta protein of Human Adenovirus E for vaccine design","volume":"39","author":"Patwary","year":"2016","journal-title":"Biomed. J."},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Moody, R., Wilson, K.L., Boer, J.C., Holien, J.K., Flanagan, K.L., Jaworowski, A., and Plebanski, M. (2021). Predicted B Cell Epitopes Highlight the Potential for COVID-19 to Drive Self-Reactive Immunity. Front. Bioinform., 1.","DOI":"10.3389\/fbinf.2021.709533"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"W502","DOI":"10.1093\/nar\/gkz452","article-title":"IEDB-AR: Immune epitope database\u2014Analysis resource in 2019","volume":"47","author":"Dhanda","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_76","unstructured":"Meza, J.A. (2024). Developing A Novel SARS-COV-2 DNA Vaccine to Elicit an Adaptive Immune Response Using A Padre Motif. [Master\u2019s Thesis, Johns Hopkins University]."},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Chauhan, V., Rungta, T., Goyal, K., and Singh, M.P. (2019). Designing a multi-epitope based vaccine to combat Kaposi Sarcoma utilizing immunoinformatics approach. Sci. Rep., 9.","DOI":"10.1038\/s41598-019-39299-8"},{"key":"ref_78","doi-asserted-by":"crossref","unstructured":"Aiman, S., Alhamhoom, Y., Ali, F., Rahman, N., Rastrelli, L., Khan, A., Farooq, Q.u.A., Ahmed, A., Khan, A., and Li, C. (2022). Multi-epitope chimeric vaccine design against emerging Monkeypox virus via reverse vaccinology techniques\u2014A bioinformatics and immunoinformatics approach. Front. Immunol., 13.","DOI":"10.3389\/fimmu.2022.985450"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1021\/acs.jcim.9b01051","article-title":"Multiepitope subunit vaccine to evoke immune response against acute encephalitis","volume":"60","author":"Kumar","year":"2019","journal-title":"J. Chem. Inf. Model."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"6292","DOI":"10.1080\/07391102.2023.2233627","article-title":"Immunoinformatic-guided novel mRNA vaccine designing to elicit immunogenic responses against the endemic Monkeypox virus","volume":"42","author":"Aiman","year":"2024","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"1544","DOI":"10.1126\/science.291.5508.1544","article-title":"Induction of direct antimicrobial activity through mammalian toll-like receptors","volume":"291","author":"Stenger","year":"2001","journal-title":"Science"},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Monterrubio-L\u00f3pez, G.P., Gonz\u00e1lez-Y-Merchand, J.A., and Ribas-Aparicio, R.M. (2015). Identification of novel potential vaccine candidates against tuberculosis based on reverse vaccinology. BioMed Res. Int., 2015.","DOI":"10.1155\/2015\/483150"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1080\/14728222.2017.1299128","article-title":"Implications of Toll-like receptors in Ebola infection","volume":"21","author":"Saghazadeh","year":"2017","journal-title":"Expert Opin. Ther. Targets"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"811","DOI":"10.2217\/fvl.14.70","article-title":"Novel drugs targeting Toll-like receptors for antiviral therapy","volume":"9","author":"Patel","year":"2014","journal-title":"Future Virol."},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Mahafujul Alam, S.S., Mir, S.A., Samanta, A., Nayak, B., Ali, S., and Hoque, M. (2025). Immunoinformatics based designing of a multi-epitope cancer vaccine targeting programmed cell death ligand 1. Sci. Rep., 15.","DOI":"10.1038\/s41598-025-87063-y"},{"key":"ref_86","doi-asserted-by":"crossref","unstructured":"Bhattacharya, K., Shamkh, I.M., Khan, M.S., Lotfy, M.M., Nzeyimana, J.B., Abutayeh, R.F., Hamdy, N.M., Hamza, D., Chanu, N.R., and Khanal, P. (2022). Multi-epitope vaccine design against monkeypox virus via reverse vaccinology method exploiting immunoinformatic and bioinformatic approaches. Vaccines, 10.","DOI":"10.3390\/vaccines10122010"},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Tahir ul Qamar, M., Rehman, A., Tusleem, K., Ashfaq, U.A., Qasim, M., Zhu, X., Fatima, I., Shahid, F., and Chen, L.-L. (2020). Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics and in silico approaches. PLoS ONE, 15.","DOI":"10.1101\/2020.02.28.970343"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"4288","DOI":"10.1039\/D1RA06532G","article-title":"Design of a multi-epitope vaccine against SARS-CoV-2: Immunoinformatic and computational methods","volume":"12","author":"Rafi","year":"2022","journal-title":"RSC Adv."},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1016\/j.biotechadv.2011.09.013","article-title":"Bacterial expression systems for recombinant protein production: E. coli and beyond","volume":"30","author":"Chen","year":"2012","journal-title":"Biotechnol. Adv."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.gene.2016.02.047","article-title":"Synonymous codon usage pattern in glycoprotein gene of rabies virus","volume":"584","author":"Morla","year":"2016","journal-title":"Gene"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"e2128391","DOI":"10.1001\/jamanetworkopen.2021.28391","article-title":"Coverage and estimated effectiveness of mRNA COVID-19 vaccines among US veterans","volume":"4","author":"Korves","year":"2021","journal-title":"JAMA Netw. Open"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1586\/14760584.3.1.59","article-title":"Genome-derived vaccines","volume":"3","author":"Groot","year":"2004","journal-title":"Expert Rev. Vaccines"},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Flower, D.R., Macdonald, I.K., Ramakrishnan, K., Davies, M.N., and Doytchinova, I.A. (2010). Computer aided selection of candidate vaccine antigens. Immunome Res., 1\u201316.","DOI":"10.1186\/1745-7580-6-S2-S1"},{"key":"ref_94","doi-asserted-by":"crossref","unstructured":"Patronov, A., and Doytchinova, I. (2013). T-cell epitope vaccine design by immunoinformatics. Open Biol., 3.","DOI":"10.1098\/rsob.120139"}],"container-title":["Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-7737\/14\/7\/830\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T18:06:36Z","timestamp":1760033196000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-7737\/14\/7\/830"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,7,8]]},"references-count":94,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2025,7]]}},"alternative-id":["biology14070830"],"URL":"https:\/\/doi.org\/10.3390\/biology14070830","relation":{},"ISSN":["2079-7737"],"issn-type":[{"value":"2079-7737","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,7,8]]}}}