{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T19:50:46Z","timestamp":1792785046690,"version":"4.5.0"},"reference-count":82,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T00:00:00Z","timestamp":1782345600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":85,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"The authors extend their appreciation to the Deanship of Research and Graduate Studies at King Khalid University for funding this work through Large Research Project under grant number .\"","award":["RGP2\/195\/47"],"award-info":[{"award-number":["RGP2\/195\/47"]}],"id":[{"id":"https:\/\/ror.org\/052kwzs30","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Sci Rep"],"DOI":"10.1038\/s41598-026-59273-5","type":"journal-article","created":{"date-parts":[[2026,6,25]],"date-time":"2026-06-25T04:24:57Z","timestamp":1782361497000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Development of an Env based HIV mRNA vaccine through immunoinformatics and computational modeling"],"prefix":"10.1038","volume":"16","author":[{"given":"Akmal","family":"Zubair","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maded","family":"Aldohri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faisal","family":"Ahmad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muhammad Yaqoob","family":"Shahani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naila","family":"Afghan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,6,25]]},"reference":[{"key":"59273_CR1","unstructured":"HIV.gov. HIV Health & Wellness, Overview, Data, and Global Statistics. (2025). Available from: https:\/\/www.hiv.gov\/hiv-basics\/overview\/data-and-trends\/global-statistics"},{"issue":"5","key":"59273_CR2","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1007\/s10142-024-01425-9","volume":"24","author":"A Zubair","year":"2024","unstructured":"Zubair, A. et al. Clinical trials and recent progress in HIV vaccine development. Funct. Integr. Genom. 24 (5), 143 (2024).","journal-title":"Funct. Integr. Genom."},{"issue":"6","key":"59273_CR3","doi-asserted-by":"publisher","first-page":"824","DOI":"10.1111\/hiv.70024","volume":"26","author":"A Zubair","year":"2025","unstructured":"Zubair, A. et al. mRNA vaccines against HIV: Hopes and challenges. HIV Med. 26 (6), 824\u2013838 (2025).","journal-title":"HIV Med."},{"key":"59273_CR4","unstructured":"Health, N. I. HIV treatment: The basics. Avail\u2013able at: (2019). https:\/\/hivinfo.nih.gov\/understanding\u2013hiv\/fact\u2013sheets\/hiv\u2013treatment\u2013basics (Accessed on: 27\/5\/2022)."},{"key":"59273_CR5","doi-asserted-by":"crossref","unstructured":"Latif, K. et al. Integrative immunoinformatics and molecular modeling approaches for the rational design and in silico validation of a multi-epitope vaccine candidate against human herpesvirus 7 (Naunyn-Schmiedeberg\u2019s Archives of Pharmacology, 2026).","DOI":"10.1007\/s00210-026-05258-0"},{"issue":"3","key":"59273_CR6","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1007\/s40203-025-00428-z","volume":"13","author":"IU Haq","year":"2025","unstructured":"Haq, I. U. et al. Using immunoinformatics and bioinformatics approach to design novel and effective rational in-silico vaccine against human Astrovirus targeting the capsid polyprotein VP90: a silent threat to global gastrointestinal tract. Silico Pharmacol. 13 (3), 139 (2025).","journal-title":"Silico Pharmacol."},{"key":"59273_CR7","unstructured":"Bertozzi, S. et al. HIV\/AIDS prevention and treatment. (2011)."},{"key":"59273_CR8","doi-asserted-by":"publisher","unstructured":"Ullah, N., Haq, I. U., Rahiyab, M., Ali, S. S., Khan, I., & Iqbal, A. (2026). In-silico design of a novel multi-epitope vaccine against Chapare virus using integrated immunoinformatics and bioinformatics approaches. Medicine in Omics, 100059. https:\/\/doi.org\/10.1016\/j.meomic.2026.100059","DOI":"10.1016\/j.meomic.2026.100059"},{"issue":"3","key":"59273_CR9","doi-asserted-by":"publisher","first-page":"500463","DOI":"10.1016\/j.vacune.2025.500463","volume":"26","author":"M Rahiyab","year":"2025","unstructured":"Rahiyab, M. et al. Design of a new multi-epitope subunit vaccine to combat the EIA virus, targeting Pol, Gag, and Env proteins: In silico technique. Vacunas (English Edition). 26 (3), 500463 (2025).","journal-title":"Vacunas (English Edition)"},{"issue":"4","key":"59273_CR10","doi-asserted-by":"publisher","first-page":"a007161","DOI":"10.1101\/cshperspect.a007161","volume":"2","author":"EJ Arts","year":"2012","unstructured":"Arts, E. J. & Hazuda, D. J. HIV-1 antiretroviral drug therapy. Cold Spring Harbor Perspect. Med. 2 (4), a007161 (2012).","journal-title":"Cold Spring Harbor Perspect. Med."},{"issue":"1","key":"59273_CR11","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1089\/apc.2023.0178","volume":"38","author":"ES Nawfal","year":"2024","unstructured":"Nawfal, E. S. et al. A systematic review of the impact of HIV-related stigma and serostatus disclosure on retention in care and antiretroviral therapy adherence among women with HIV in the United States\/Canada. AIDS Patient Care STDs. 38 (1), 23\u201349 (2024).","journal-title":"AIDS Patient Care STDs"},{"issue":"1","key":"59273_CR12","doi-asserted-by":"publisher","first-page":"1642","DOI":"10.1038\/s41598-024-52142-z","volume":"14","author":"T Gebru","year":"2024","unstructured":"Gebru, T. et al. Prevalence of depression and associated factors among HIV\/AIDS patients attending antiretroviral therapy clinic at Adama Hospital Medical College, Adama, Central Ethiopia. Sci. Rep. 14 (1), 1642 (2024).","journal-title":"Sci. Rep."},{"key":"59273_CR13","doi-asserted-by":"crossref","unstructured":"Zubair, A. et al. Current Challenges With Highly Active Antiretroviral Therapy and New Hope and Horizon With CRISPR-CAS9 Technology for HIV Treatment Vol. 105, p. e70121 (Chemical Biology & Drug Design, 2025). 5.","DOI":"10.1111\/cbdd.70121"},{"issue":"3","key":"59273_CR14","doi-asserted-by":"publisher","first-page":"324","DOI":"10.1007\/s11262-025-02149-z","volume":"61","author":"A Zubair","year":"2025","unstructured":"Zubair, A. et al. Molecular characterization and drug resistance pattern in pol gene of HIV-1 sub-subtypes circulating in Lahore, Pakistan. Virus Genes. 61 (3), 324\u2013341 (2025).","journal-title":"Virus Genes"},{"issue":"1","key":"59273_CR15","doi-asserted-by":"publisher","first-page":"108","DOI":"10.1007\/s10142-025-01613-1","volume":"25","author":"HM Hassan","year":"2025","unstructured":"Hassan, H. M. et al. New hope and promise with CRISPR-Cas9 technology for the treatment of HIV. Funct. Integr. Genom. 25 (1), 108 (2025).","journal-title":"Funct. Integr. Genom."},{"key":"59273_CR16","doi-asserted-by":"publisher","first-page":"e25793","DOI":"10.1002\/jia2.25793","volume":"24","author":"J Kim","year":"2021","unstructured":"Kim, J. et al. Current approaches to HIV vaccine development: a narrative review. J. Int. AIDS. Soc. 24, e25793 (2021).","journal-title":"J. Int. AIDS. Soc."},{"issue":"2","key":"59273_CR17","doi-asserted-by":"publisher","first-page":"100619","DOI":"10.1016\/j.hlpt.2022.100619","volume":"11","author":"JE Harris","year":"2022","unstructured":"Harris, J. E. The repeated setbacks of HIV vaccine development laid the groundwork for SARS-CoV-2 vaccines. Health policy Technol. 11 (2), 100619 (2022).","journal-title":"Health policy Technol."},{"key":"59273_CR18","doi-asserted-by":"publisher","first-page":"e944600","DOI":"10.12659\/MSM.944600","volume":"30","author":"DV Parums","year":"2024","unstructured":"Parums, D. V. Forty Years of Waiting for Prevention and Cure of HIV Infection\u2013Ongoing Challenges and Hopes for Vaccine Development and Overcoming Antiretroviral Drug Resistance. Med. Sci. Monitor: Int. Med. J. Experimental Clin. Res. 30, e944600\u2013e944601 (2024).","journal-title":"Med. Sci. Monitor: Int. Med. J. Experimental Clin. Res."},{"issue":"3","key":"59273_CR19","first-page":"40","volume":"37","author":"J Yue","year":"2023","unstructured":"Yue, J. et al. The R&D landscape for infectious disease vaccines. infection 37 (3), 40 (2023).","journal-title":"infection"},{"issue":"1","key":"59273_CR20","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1038\/s41541-022-00503-y","volume":"7","author":"T Travieso","year":"2022","unstructured":"Travieso, T. et al. The use of viral vectors in vaccine development. npj Vaccines. 7 (1), 75 (2022).","journal-title":"npj Vaccines"},{"issue":"3","key":"59273_CR21","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1021\/acsabm.1c01238","volume":"5","author":"IW Hamley","year":"2022","unstructured":"Hamley, I. W. Peptides for vaccine development. ACS Appl. Bio Mater. 5 (3), 905\u2013944 (2022).","journal-title":"ACS Appl. Bio Mater."},{"issue":"1","key":"59273_CR22","doi-asserted-by":"publisher","first-page":"4645","DOI":"10.1038\/s41598-022-08506-4","volume":"12","author":"H Al Tbeishat","year":"2022","unstructured":"Al Tbeishat, H. Novel In Silico mRNA vaccine design exploiting proteins of M. tuberculosis that modulates host immune responses by inducing epigenetic modifications. Sci. Rep. 12 (1), 4645 (2022).","journal-title":"Sci. Rep."},{"key":"59273_CR23","doi-asserted-by":"publisher","first-page":"1480025","DOI":"10.3389\/fimmu.2025.1480025","volume":"16","author":"MZ Ahmed","year":"2025","unstructured":"Ahmed, M. Z. et al. Immunoinformatic-driven design and evaluation of multi-epitope mRNA vaccine targeting HIV-1 gp120. Front. Immunol. 16, 1480025 (2025).","journal-title":"Front. Immunol."},{"issue":"2","key":"59273_CR24","first-page":"407","volume":"70","author":"M Naveed","year":"2023","unstructured":"Naveed, M. et al. A reverse vaccinology approach to design an mRNA-based vaccine to provoke a robust immune response against HIV-1. Acta Biochim. Pol. 70 (2), 407\u2013418 (2023).","journal-title":"Acta Biochim. Pol."},{"issue":"9","key":"59273_CR25","doi-asserted-by":"publisher","first-page":"e0307877","DOI":"10.1371\/journal.pone.0307877","volume":"19","author":"H Shi","year":"2024","unstructured":"Shi, H. et al. Development of innovative multi-epitope mRNA vaccine against central nervous system tuberculosis using in silico approaches. Plos one. 19 (9), e0307877 (2024).","journal-title":"Plos one"},{"issue":"2","key":"59273_CR26","doi-asserted-by":"publisher","first-page":"e150","DOI":"10.15190\/d.2022.9","volume":"10","author":"A Fortner","year":"2022","unstructured":"Fortner, A. & Bucur, O. mRNA-based vaccine technology for HIV. Discoveries 10 (2), e150 (2022).","journal-title":"Discoveries"},{"issue":"3","key":"59273_CR27","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1007\/s12026-022-09351-3","volume":"71","author":"Y Mohammadi","year":"2023","unstructured":"Mohammadi, Y. et al. In silico design and evaluation of a novel mRNA vaccine against BK virus: a reverse vaccinology approach. Immunol. Res. 71 (3), 422\u2013441 (2023).","journal-title":"Immunol. Res."},{"issue":"5","key":"59273_CR28","doi-asserted-by":"publisher","first-page":"1120","DOI":"10.3390\/v15051120","volume":"15","author":"N Rcheulishvili","year":"2023","unstructured":"Rcheulishvili, N. et al. Development of a multi-epitope universal mRNA vaccine candidate for monkeypox, smallpox, and vaccinia viruses: design and in silico analyses. Viruses 15 (5), 1120 (2023).","journal-title":"Viruses"},{"issue":"8","key":"59273_CR29","doi-asserted-by":"publisher","first-page":"e1360","DOI":"10.1002\/iid3.1360","volume":"12","author":"EK Oladipo","year":"2024","unstructured":"Oladipo, E. K. et al. Exploring computational approaches to design mRNA Vaccine against vaccinia and Mpox viruses. Immun. Inflamm. Dis. 12 (8), e1360 (2024).","journal-title":"Immun. Inflamm. Dis."},{"issue":"10","key":"59273_CR30","doi-asserted-by":"publisher","first-page":"e0309560","DOI":"10.1371\/journal.pone.0309560","volume":"19","author":"Y Zhu","year":"2024","unstructured":"Zhu, Y. et al. Novel dual-pathogen multi-epitope mRNA vaccine development for Brucella melitensis and Mycobacterium tuberculosis in silico approach. Plos one. 19 (10), e0309560 (2024).","journal-title":"Plos one"},{"issue":"D1","key":"59273_CR31","doi-asserted-by":"publisher","first-page":"D10","DOI":"10.1093\/nar\/gkaa892","volume":"49","author":"EW Sayers","year":"2021","unstructured":"Sayers, E. W. et al. Database resources of the national center for biotechnology information. Nucleic Acids Res. 49 (D1), D10\u2013D17 (2021).","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"59273_CR32","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1186\/1471-2105-8-4","volume":"8","author":"IA Doytchinova","year":"2007","unstructured":"Doytchinova, I. A. & Flower, D. R. VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinform. 8 (1), 4 (2007).","journal-title":"BMC Bioinform."},{"issue":"1","key":"59273_CR33","doi-asserted-by":"publisher","first-page":"424","DOI":"10.1186\/1471-2105-8-424","volume":"8","author":"MV Larsen","year":"2007","unstructured":"Larsen, M. V. et al. Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinform. 8 (1), 424 (2007).","journal-title":"BMC Bioinform."},{"issue":"W1","key":"59273_CR34","doi-asserted-by":"publisher","first-page":"W449","DOI":"10.1093\/nar\/gkaa379","volume":"48","author":"B Reynisson","year":"2020","unstructured":"Reynisson, B. et al. NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Res. 48 (W1), W449\u2013W454 (2020).","journal-title":"Nucleic Acids Res."},{"key":"59273_CR35","doi-asserted-by":"publisher","first-page":"102215","DOI":"10.1016\/j.coi.2022.102215","volume":"77","author":"JJ Baljon","year":"2022","unstructured":"Baljon, J. J. & Wilson, J. T. Bioinspired vaccines to enhance MHC class-I antigen cross-presentation. Curr. Opin. Immunol. 77, 102215 (2022).","journal-title":"Curr. Opin. Immunol."},{"issue":"D1","key":"59273_CR36","doi-asserted-by":"publisher","first-page":"D339","DOI":"10.1093\/nar\/gky1006","volume":"47","author":"R Vita","year":"2019","unstructured":"Vita, R. et al. The immune epitope database (IEDB): 2018 update. Nucleic Acids Res. 47 (D1), D339\u2013D343 (2019).","journal-title":"Nucleic Acids Res."},{"issue":"1","key":"59273_CR37","first-page":"2680160","volume":"2017","author":"JL Sanchez-Trincado","year":"2017","unstructured":"Sanchez-Trincado, J. L., Gomez-Perosanz, M. & Reche, P. A. Fundamentals and methods for T-and B\u2010cell epitope prediction. J. Immunol. Res. 2017 (1), 2680160 (2017).","journal-title":"J. Immunol. Res."},{"key":"59273_CR38","doi-asserted-by":"crossref","unstructured":"Oladipo, E. K. et al. Immunoinformatics-Based Strategies for mRNA Vaccine Development against Ilesha Virus. In Silico Research in Biomedicine, p. 100046. (2025).","DOI":"10.1016\/j.insi.2025.100046"},{"issue":"7","key":"59273_CR39","doi-asserted-by":"publisher","first-page":"117","DOI":"10.3390\/computation10070117","volume":"10","author":"OO Oluwagbemi","year":"2022","unstructured":"Oluwagbemi, O. O. et al. Bioinformatics, computational informatics, and modeling approaches to the design of mRNA COVID-19 vaccine candidates. Computation 10 (7), 117 (2022).","journal-title":"Computation"},{"issue":"20","key":"59273_CR40","doi-asserted-by":"publisher","first-page":"9612","DOI":"10.1073\/pnas.89.20.9612","volume":"89","author":"F Lejbkowicz","year":"1992","unstructured":"Lejbkowicz, F. et al. A fraction of the mRNA 5\u2019cap-binding protein, eukaryotic initiation factor 4E, localizes to the nucleus. Proc. Natl. Acad. Sci. 89 (20), 9612\u20139616 (1992).","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"1","key":"59273_CR41","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1080\/14760584.2021.1991794","volume":"21","author":"D Mekonnen","year":"2022","unstructured":"Mekonnen, D., Mengist, H. M. & Jin, T. SARS-CoV-2 subunit vaccine adjuvants and their signaling pathways. Expert Rev. Vaccines. 21 (1), 69\u201381 (2022).","journal-title":"Expert Rev. Vaccines"},{"issue":"1","key":"59273_CR42","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1186\/s12865-024-00668-2","volume":"25","author":"EK Oladipo","year":"2024","unstructured":"Oladipo, E. K. et al. Bioinformatics designing of an mRNA vaccine for Mokola virus (MOKV) using immunoinformatics as a secure strategy for successful vaccine development. BMC Immunol. 25 (1), 77 (2024).","journal-title":"BMC Immunol."},{"issue":"1","key":"59273_CR43","doi-asserted-by":"publisher","first-page":"166","DOI":"10.1038\/s41392-022-01007-w","volume":"7","author":"S Qin","year":"2022","unstructured":"Qin, S. et al. mRNA-based therapeutics: powerful and versatile tools to combat diseases. Signal. Transduct. Target. therapy. 7 (1), 166 (2022).","journal-title":"Signal. Transduct. Target. therapy"},{"issue":"6","key":"59273_CR44","doi-asserted-by":"publisher","first-page":"2278","DOI":"10.1007\/s00894-014-2278-5","volume":"20","author":"I Dimitrov","year":"2014","unstructured":"Dimitrov, I. et al. AllerTOP v. 2\u2014a server for in silico prediction of allergens. J. Mol. Model. 20 (6), 2278 (2014).","journal-title":"J. Mol. Model."},{"key":"59273_CR45","doi-asserted-by":"publisher","first-page":"bbac174","DOI":"10.1093\/bib\/bbac174","volume":"23","author":"N Sharma","year":"2022","unstructured":"Sharma, N. et al. ToxinPred2: an improved method for predicting toxicity of proteins. Briefings Bioinf. vol. 23, bbac174. (2022). https:\/\/doi.org\/10.1093\/bib\/bbac174","journal-title":"Briefings Bioinf. vol"},{"key":"59273_CR46","doi-asserted-by":"crossref","unstructured":"Gasteiger, E. et al. Protein identification and analysis tools on the ExPASy server, in The proteomics protocols handbook p. 571\u2013607 (Springer, 2005).","DOI":"10.1385\/1-59259-890-0:571"},{"issue":"19","key":"59273_CR47","doi-asserted-by":"publisher","first-page":"3098","DOI":"10.1093\/bioinformatics\/btx345","volume":"33","author":"M Hebditch","year":"2017","unstructured":"Hebditch, M. et al. Protein\u2013Sol: a web tool for predicting protein solubility from sequence. Bioinformatics 33 (19), 3098\u20133100 (2017).","journal-title":"Bioinformatics"},{"issue":"24","key":"59273_CR48","doi-asserted-by":"publisher","first-page":"3991","DOI":"10.1093\/bioinformatics\/btx521","volume":"33","author":"G Del\u00e9age","year":"2017","unstructured":"Del\u00e9age, G. ALIGNSEC: viewing protein secondary structure predictions within large multiple sequence alignments. Bioinformatics 33 (24), 3991\u20133992 (2017).","journal-title":"Bioinformatics"},{"issue":"W1","key":"59273_CR49","doi-asserted-by":"publisher","first-page":"W296","DOI":"10.1093\/nar\/gky427","volume":"46","author":"A Waterhouse","year":"2018","unstructured":"Waterhouse, A. et al. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46 (W1), W296\u2013W303 (2018).","journal-title":"Nucleic Acids Res."},{"issue":"2","key":"59273_CR50","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1107\/S0021889892009944","volume":"26","author":"RA Laskowski","year":"1993","unstructured":"Laskowski, R. A. et al. PROCHECK: a program to check the stereochemical quality of protein structures. Appl. Crystallogr. 26 (2), 283\u2013291 (1993).","journal-title":"Appl. Crystallogr."},{"issue":"1","key":"59273_CR51","doi-asserted-by":"publisher","first-page":"1157023","DOI":"10.1155\/2021\/1157023","volume":"2021","author":"AS Sameer","year":"2021","unstructured":"Sameer, A. S. & Nissar, S. Toll-like receptors (TLRs): structure, functions, signaling, and role of their polymorphisms in colorectal cancer susceptibility. Biomed. Res. Int. 2021 (1), 1157023 (2021).","journal-title":"Biomed. Res. Int."},{"issue":"2","key":"59273_CR52","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1038\/nprot.2016.169","volume":"12","author":"D Kozakov","year":"2017","unstructured":"Kozakov, D. et al. The ClusPro web server for protein\u2013protein docking. Nat. Protoc. 12 (2), 255\u2013278 (2017).","journal-title":"Nat. Protoc."},{"issue":"W1","key":"59273_CR53","doi-asserted-by":"publisher","first-page":"W271","DOI":"10.1093\/nar\/gku339","volume":"42","author":"JR L\u00f3pez-Blanco","year":"2014","unstructured":"L\u00f3pez-Blanco, J. R. et al. iMODS: internal coordinates normal mode analysis server. Nucleic Acids Res. 42 (W1), W271\u2013W276 (2014).","journal-title":"Nucleic Acids Res."},{"issue":"4","key":"59273_CR54","doi-asserted-by":"publisher","first-page":"e9862","DOI":"10.1371\/journal.pone.0009862","volume":"5","author":"N Rapin","year":"2010","unstructured":"Rapin, N. et al. Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system. PloS one. 5 (4), e9862 (2010).","journal-title":"PloS one"},{"issue":"1","key":"59273_CR55","doi-asserted-by":"publisher","first-page":"9232","DOI":"10.1038\/s41598-017-09199-w","volume":"7","author":"M Ali","year":"2017","unstructured":"Ali, M. et al. Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection. Sci. Rep. 7 (1), 9232 (2017).","journal-title":"Sci. Rep."},{"issue":"1","key":"59273_CR56","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/1748-7188-6-26","volume":"6","author":"R Lorenz","year":"2011","unstructured":"Lorenz, R. et al. ViennaRNA Package 2.0. Algorithms Mol. biology. 6 (1), 26 (2011).","journal-title":"Algorithms Mol. biology"},{"issue":"Web Server issu","key":"59273_CR57","doi-asserted-by":"publisher","first-page":"W526","DOI":"10.1093\/nar\/gki376","volume":"33","author":"A Grote","year":"2005","unstructured":"Grote, A. et al. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res. 33 (Web Server issue), W526\u2013W531 (2005).","journal-title":"Nucleic Acids Res."},{"key":"59273_CR58","doi-asserted-by":"publisher","first-page":"106635","DOI":"10.1016\/j.fitote.2025.106635","volume":"184","author":"MA Mbock","year":"2025","unstructured":"Mbock, M. A. et al. Safety assessment of Detarium microcarpum Guil. & Perr. (Leguminosae) root bark extract in rats: Acute, sub-acute toxicity, ADMET, molecular docking, and molecular dynamics simulations approach. Fitoterapia 184, 106635 (2025).","journal-title":"Fitoterapia"},{"issue":"2","key":"59273_CR59","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1007\/s40203-024-00278-1","volume":"12","author":"KA Oluwafemi","year":"2024","unstructured":"Oluwafemi, K. A. et al. Investigating the effect of 1,2-Dibenzoylhydrazine on Staphylococcus aureus using integrated computational approaches. Silico Pharmacol. 12 (2), 102 (2024).","journal-title":"Silico Pharmacol."},{"issue":"8","key":"59273_CR60","doi-asserted-by":"publisher","first-page":"e0290576","DOI":"10.1371\/journal.pone.0290576","volume":"18","author":"S Ullah","year":"2023","unstructured":"Ullah, S. et al. A computational approach to fighting type 1 diabetes by targeting 2\u00a0C Coxsackie B virus protein with flavonoids. PLOS ONE. 18 (8), e0290576 (2023).","journal-title":"PLOS ONE"},{"issue":"1","key":"59273_CR61","doi-asserted-by":"publisher","first-page":"5426","DOI":"10.1038\/s41598-024-84401-4","volume":"15","author":"B Othman","year":"2025","unstructured":"Othman, B. et al. Comprehensive pharmacokinetic profiling and molecular docking analysis of natural bioactive compounds targeting oncogenic biomarkers in breast cancer. Sci. Rep. 15 (1), 5426 (2025).","journal-title":"Sci. Rep."},{"issue":"9","key":"59273_CR62","doi-asserted-by":"publisher","first-page":"103753","DOI":"10.1016\/j.sjbs.2023.103753","volume":"30","author":"ZK Bagewadi","year":"2023","unstructured":"Bagewadi, Z. K. et al. Molecular dynamics and simulation analysis against superoxide dismutase (SOD) target of Micrococcus luteus with secondary metabolites from Bacillus licheniformis recognized by genome mining approach. Saudi J. Biol. Sci. 30 (9), 103753 (2023).","journal-title":"Saudi J. Biol. Sci."},{"key":"59273_CR63","doi-asserted-by":"publisher","first-page":"77","DOI":"10.3390\/life11020077","volume":"11","author":"MA Rasheed","year":"2021","unstructured":"Rasheed, M. A. et al. Identification of Lead Compounds against Scm (fms10) in Enterococcus faecium Using Computer Aided Drug Designing. Life 11, 77. https:\/\/doi.org\/10.3390\/life11020077 (2021).","journal-title":"Life"},{"key":"59273_CR64","doi-asserted-by":"publisher","first-page":"124091","DOI":"10.1016\/j.ijheatmasstransfer.2023.124091","volume":"208","author":"H Sun","year":"2023","unstructured":"Sun, H. et al. Molecular dynamics study on the role of hydrogen bonds and interfacial heat transfer between diverse silica surfaces and organic liquids. Int. J. Heat Mass Transf. 208, 124091 (2023).","journal-title":"Int. J. Heat Mass Transf."},{"issue":"3","key":"59273_CR65","doi-asserted-by":"publisher","first-page":"500427","DOI":"10.1016\/j.vacun.2025.500427","volume":"26","author":"Najeebullah","year":"2025","unstructured":"Najeebullah et al. Rational in-silico design of a multi-epitope vaccine against human Rhinovirus an immune simulation and molecular dynamics simulation approach. Vacunas 26 (3), 500427 (2025).","journal-title":"Vacunas"},{"issue":"23","key":"59273_CR66","doi-asserted-by":"publisher","first-page":"3096","DOI":"10.1016\/j.vaccine.2017.04.031","volume":"35","author":"P Jiang","year":"2017","unstructured":"Jiang, P. et al. Evaluation of tandem Chlamydia trachomatis MOMP multi-epitopes vaccine in BALB\/c mice model. Vaccine 35 (23), 3096\u20133103 (2017).","journal-title":"Vaccine"},{"key":"59273_CR67","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1016\/j.meegid.2019.03.003","volume":"70","author":"M Hasan","year":"2019","unstructured":"Hasan, M. et al. Vaccinomics strategy for developing a unique multi-epitope monovalent vaccine against Marburg marburgvirus. Infect. Genet. Evol. 70, 140\u2013157 (2019).","journal-title":"Infect. Genet. Evol."},{"issue":"1","key":"59273_CR68","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1186\/s12985-025-02764-0","volume":"22","author":"SK Mishra","year":"2025","unstructured":"Mishra, S. K. et al. Integrated Immuno and bioinformatics assisted novel epitope vaccine against HIV infection: a study based on complete genome. Virol. J. 22 (1), 228 (2025).","journal-title":"Virol. J."},{"issue":"4","key":"59273_CR69","doi-asserted-by":"publisher","first-page":"1971","DOI":"10.1007\/s10499-022-00884-w","volume":"30","author":"H Mondal","year":"2022","unstructured":"Mondal, H. & Thomas, J. A review on the recent advances and application of vaccines against fish pathogens in aquaculture. Aquacult. Int. 30 (4), 1971\u20132000 (2022).","journal-title":"Aquacult. Int."},{"key":"59273_CR70","unstructured":"Kaper, J., Rappuoli, R. & Buckley, M. Vaccine development: current status and future needs. (2005)."},{"issue":"4","key":"59273_CR71","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1038\/s41591-021-01301-0","volume":"27","author":"JL Excler","year":"2021","unstructured":"Excler, J. L. et al. Vaccine development for emerging infectious diseases. Nat. Med. 27 (4), 591\u2013600 (2021).","journal-title":"Nat. Med."},{"issue":"1","key":"59273_CR72","doi-asserted-by":"publisher","first-page":"19707","DOI":"10.1038\/s41598-021-99227-7","volume":"11","author":"AO Fadaka","year":"2021","unstructured":"Fadaka, A. O. et al. Immunoinformatics design of a novel epitope-based vaccine candidate against dengue virus. Sci. Rep. 11 (1), 19707 (2021).","journal-title":"Sci. Rep."},{"issue":"2","key":"59273_CR73","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1038\/cmi.2017.92","volume":"15","author":"L Zhang","year":"2018","unstructured":"Zhang, L. Multi-epitope vaccines: a promising strategy against tumors and viral infections. Cell Mol. Immunol. 15 (2), 182\u2013184 (2018).","journal-title":"Cell Mol. Immunol."},{"key":"59273_CR74","doi-asserted-by":"publisher","first-page":"590780","DOI":"10.3389\/fimmu.2020.590780","volume":"11","author":"T Ng\u2019uni","year":"2020","unstructured":"Ng\u2019uni, T., Chasara, C. & Ndhlovu, Z. M. Major Scientific Hurdles in HIV Vaccine Development: Historical Perspective and Future Directions. Front. Immunol. 11, 590780 (2020).","journal-title":"Front. Immunol."},{"issue":"4","key":"59273_CR75","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1038\/nrd.2017.243","volume":"17","author":"N Pardi","year":"2018","unstructured":"Pardi, N. et al. mRNA vaccines\u2014a new era in vaccinology. Nat. Rev. Drug Discovery. 17 (4), 261\u2013279 (2018).","journal-title":"Nat. Rev. Drug Discovery"},{"issue":"2","key":"59273_CR76","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1111\/j.1365-2567.2007.02651.x","volume":"122","author":"G Liu","year":"2007","unstructured":"Liu, G. & Zhao, Y. Toll-like receptors and immune regulation: their direct and indirect modulation on regulatory CD4\u2009+\u2009CD25+ T cells. Immunology 122 (2), 149\u2013156 (2007).","journal-title":"Immunology"},{"key":"59273_CR77","doi-asserted-by":"publisher","unstructured":"Masenga, Sepiso, K. et al. HIV-Host Cell Interactions. Cells 12,10 1351. (2023). https:\/\/doi.org\/10.3390\/cells12101351","DOI":"10.3390\/cells12101351"},{"issue":"1","key":"59273_CR78","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12985-025-03026-9","volume":"23","author":"SK Mishra","year":"2025","unstructured":"Mishra, S. K. et al. Decoding cross-talk between Mpox and HIV: insights from transcriptomics and network-based analyses. Virol. J. 23 (1), 1 (2025).","journal-title":"Virol. J."},{"issue":"5","key":"59273_CR79","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1038\/s41435-022-00175-7","volume":"23","author":"LY Lin","year":"2022","unstructured":"Lin, L. Y. et al. Fc receptors and the diversity of antibody responses to HIV infection and vaccination. Genes Immun. 23 (5), 149\u2013156 (2022).","journal-title":"Genes Immun."},{"issue":"10","key":"59273_CR80","doi-asserted-by":"publisher","first-page":"5889","DOI":"10.1128\/JVI.77.10.5889-5901.2003","volume":"77","author":"R Pantophlet","year":"2003","unstructured":"Pantophlet, R., Wilson, I. A. & Burton, D. R. Hyperglycosylated mutants of human immunodeficiency virus (HIV) type 1 monomeric gp120 as novel antigens for HIV vaccine design. J. Virol. 77 (10), 5889\u20135901 (2003).","journal-title":"J. Virol."},{"key":"59273_CR81","doi-asserted-by":"publisher","unstructured":"Ringe, R. P. et al. Jul. Reducing V3 Antigenicity and Immunogenicity on Soluble, Native-Like HIV-1 Env SOSIP Trimers. Journal of virology vol. 91,15 e00677-17 (2017). https:\/\/doi.org\/10.1128\/JVI.00677-17","DOI":"10.1128\/JVI.00677-17"},{"issue":"6759","key":"59273_CR82","doi-asserted-by":"publisher","first-page":"eadr8382","DOI":"10.1126\/science.adr8382","volume":"389","author":"JR Willis","year":"2025","unstructured":"Willis, J. R. et al. Vaccination with mRNA-encoded nanoparticles drives early maturation of HIV bnAb precursors in humans. Science 389 (6759), eadr8382 (2025).","journal-title":"Science"}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-59273-5","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-59273-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-59273-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T12:02:11Z","timestamp":1789732931000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41598-026-59273-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,6,25]]},"references-count":82,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["59273"],"URL":"https:\/\/doi.org\/10.1038\/s41598-026-59273-5","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,6,25]]},"assertion":[{"value":"30 March 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 June 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 June 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 interests","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not relevant. Additionally, neither human nor animal subjects are included in this study. The research does not require the personal information of patients. Every method was used in compliance with the relevant laws and guidelines.","order":2,"name":"Ethics","label":"<b>Ethics approval<\/b>","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Human research\n                      . This study does not involve any human or animal subjects.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The datasets used and\/or analysed during the current study available from the corresponding author on reasonable request.","order":4,"name":"Ethics","label":"Data and resources are available","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"29146"}}