{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T17:41:07Z","timestamp":1792777267209,"version":"4.5.0"},"reference-count":110,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T00:00:00Z","timestamp":1792713600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    Marburg virus disease (MVD), a deadly zoonotic illness in humans, is caused by the Marburg virus (MARV), a single-stranded RNA virus belonging to the\n                    <jats:italic>Orthomarburgvirus<\/jats:italic>\n                    genus of the\n                    <jats:italic>Filoviridae<\/jats:italic>\n                    family. There are currently no approved vaccines or efficient antiviral therapies for MARV, despite high morbidity and fatality rates of the virus, particularly in Africa. Recognizing its epidemic potential and its inclusion on the WHO list of blueprint priority pathogens, an immunoinformatics approach was used to design novel multi-epitope saRNA vaccine candidates (MB-saVaxI and MB-saVaxII) targeting the viral GP, NP, VP40, and VP35 via CD8\u2009+\u2009, CD4\u2009+\u2009, and B cell epitopes. These epitopes were derived from target protein sequences and incorporated into MB-saVaxI and MB-saVaxII after validation for antigenicity, non-allergenicity, non-toxicity, and conservation. Additionally, the selected epitopes were conjugated to suitable adjuvants via various linkers, thereby enabling the design of a potentially stable vaccine. Additionally, the designed MB-saVaxI and MB-saVaxII were incorporated into the standard saRNA model, in which ORF-2 encodes the target vaccine peptide. Moreover, biophysical analyses unveiled that the developed vaccines are basic (pI\u2009&lt;\u20097), soluble (GRAVY\u2009&lt;\u20090), and stable (aliphatic index\u2009&lt;\u200980). Subsequently, docking of MB-saVaxI to TLR2 (\u2212938.3) and TLR4 (\u2212902.4), and MB-saVaxII to TLR3 (\u22121485.4) and TLR7 (\u22121543.6) demonstrated significant affinity, with detailed hydrogen-bond interactions validated by MM-GBSA and molecular dynamics simulations. Furthermore, MB-saVaxI and MB-saVaxII were effectively cloned\n                    <jats:italic>in-silico<\/jats:italic>\n                    into\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    , and immune simulations indicated that the vaccines triggered robust innate and adaptive immunity, with a sustained memory response and TH cell activation, as evidenced by IFN-\u03b3 and IL-2 production. Additionally, the mRNA structure of MB-saVaxI and MB-saVaxII remained stable throughout the expression pathway in the host. However, extensive\n                    <jats:italic>in-vitro<\/jats:italic>\n                    and\n                    <jats:italic>in-vivo<\/jats:italic>\n                    studies are needed to establish the safety and efficacy of this vaccine candidate conclusively.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0361136","type":"journal-article","created":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T17:26:40Z","timestamp":1792776400000},"page":"e0361136","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Immunoinformatics and reverse vaccinology design of self-amplifying RNA vaccine against marburg virus with structural dynamics and immune simulation analysis"],"prefix":"10.1371","volume":"21","author":[{"given":"Md. Aftabur","family":"Rahman","sequence":"first","affiliation":[{"name":"Jahangirnagar University","place":["Dhaka, Bangladesh"],"department":["Department of Biotechnology and Genetic Engineering"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lamyea","family":"Kabir","sequence":"additional","affiliation":[{"name":"Jahangirnagar University","place":["Dhaka, Bangladesh"],"department":["Department of Biochemistry and Molecular Biology"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-8819-1260","authenticated-orcid":true,"given":"Nadia","family":"Ahmed","sequence":"additional","affiliation":[{"name":"North South University","place":["Dhaka, Bangladesh"],"department":["Department of Biochemistry and Biotechnology, School of Health and Life Sciences"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atish","family":"Barua","sequence":"additional","affiliation":[{"name":"Government City College","place":["Chattogram, Bangladesh"],"department":["Department of Zoology"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-3563-6150","authenticated-orcid":true,"given":"Mohammad","family":"Hasan","sequence":"additional","affiliation":[{"name":"North South University","place":["Dhaka, Bangladesh"],"department":["Department of Biochemistry and Microbiology"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-6706-8988","authenticated-orcid":true,"given":"Ahmad Abdullah","family":"Mahdeen","sequence":"additional","affiliation":[{"name":"Notre Dame University Bangladesh (NDUB)","place":["Dhaka, Bangladesh"],"department":["Department of Microbiology"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,10,23]]},"reference":[{"key":"pone.0361136.ref001","doi-asserted-by":"crossref","DOI":"10.1002\/hsr2.2270","article-title":"Can Marburg virus be sexually transmitted?","volume":"7","author":"H Karami","year":"2024","journal-title":"Health Science Reports"},{"issue":"1","key":"pone.0361136.ref002","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1186\/s12916-023-03108-x","article-title":"A mathematical model of Marburg virus disease outbreaks and the potential role of vaccination in control","volume":"21","author":"GY Qian","year":"2023","journal-title":"BMC Med"},{"issue":"1","key":"pone.0361136.ref003","article-title":"Marburg virus disease in sub saharan Africa Contemporary epidemiology and future trends","volume":"3","author":"OB Ojo","year":"2025","journal-title":"Epidemiol Public Health"},{"key":"pone.0361136.ref004","doi-asserted-by":"crossref","first-page":"106941","DOI":"10.1016\/j.ijsu.2022.106941","article-title":"Zoonotic concerns of Marburg virus: Current knowledge and counteracting strategies including One Health approach to limit animal-human interface: An update","volume":"106","author":"K Dhama","year":"2022","journal-title":"Int J Surg"},{"issue":"2","key":"pone.0361136.ref005","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1007\/s13337-025-00940-y","article-title":"Marburg virus outbreak: A global health threat, zoonotic risks, and the urgent need for international action","volume":"36","author":"S Das","year":"2025","journal-title":"Virusdisease"},{"key":"pone.0361136.ref006","doi-asserted-by":"crossref","first-page":"54483","DOI":"10.12775\/QS.2024.22.54483","article-title":"Experimental success in marburg virus vaccination","volume":"22","author":"M Dydyk","year":"2024","journal-title":"Qual Sport"},{"issue":"5","key":"pone.0361136.ref007","doi-asserted-by":"crossref","first-page":"2784","DOI":"10.1097\/MS9.0000000000003213","article-title":"Therapeutic advances in Marburg virus disease: From experimental treatments to vaccine development","volume":"87","author":"F Paison","year":"2025","journal-title":"Ann Med Surg (Lond)"},{"issue":"1","key":"pone.0361136.ref008","doi-asserted-by":"crossref","DOI":"10.1186\/s42269-023-01078-x","article-title":"Marburg virus outbreaks in Africa","volume":"47","author":"I Idris","year":"2023","journal-title":"Bull Natl Res Cent"},{"key":"pone.0361136.ref009","doi-asserted-by":"crossref","first-page":"219","DOI":"10.54117\/ijamb.v4i4.93","article-title":"Marburg virus disease: Virology, pathogenesis, diagnosis, treatment, and preventive strategies","volume":"4","author":"IH Iheukwumere","year":"2025","journal-title":"IPS Journal of Applied Microbiology and Biotechnology"},{"key":"pone.0361136.ref010","doi-asserted-by":"crossref","DOI":"10.1002\/hsr2.70669","article-title":"Marburg virus disease: A narrative review","volume":"8","author":"A Letafati","year":"2025","journal-title":"Health Science Reports"},{"key":"pone.0361136.ref011","article-title":"A review on Marburg virus: epidemiology, pathogenesis, advances in prevention and treatment","volume":"12","author":"R Chahal","year":"2025","journal-title":"European Journal of Pharmaceutical and Medical Research"},{"key":"pone.0361136.ref012","doi-asserted-by":"crossref","first-page":"100076","DOI":"10.1016\/j.soh.2024.100076","article-title":"Strengthening global health resilience: Marburg virus-like particle vaccines and the One Health approach","volume":"3","author":"RB Khadka","year":"2024","journal-title":"Sci One Health"},{"issue":"3","key":"pone.0361136.ref013","doi-asserted-by":"crossref","first-page":"49","DOI":"10.55544\/jrasb.4.3.7","article-title":"Leveraging multi-component control strategies for marburg virus suppression: A mathematical modeling approach","volume":"4","author":"JO Oladele","year":"2025","journal-title":"J Res Appl Sci Biotechnol"},{"key":"pone.0361136.ref014","article-title":"A highly attenuated Vesiculovax vaccine rapidly protects nonhuman primates against lethal Marburg virus challenge","author":"C Woolsey","year":"2022","journal-title":"bioRxiv"},{"issue":"2","key":"pone.0361136.ref015","doi-asserted-by":"crossref","DOI":"10.35500\/jghs.2025.7.e30","article-title":"Document analysis in Marburg virus outbreak response reports in Africa (2021\u20132025) to guide future manual updates","volume":"7","author":"VA Kyuta","year":"2025","journal-title":"J Glob Health Sci"},{"key":"pone.0361136.ref016","doi-asserted-by":"crossref","first-page":"100094","DOI":"10.1016\/j.ijidoh.2025.100094","article-title":"Comparative epidemiological analysis of the 2023 and 2025 Marburg virus disease outbreaks in Kagera Region, Tanzania","volume":"10","author":"S Rugarabamu","year":"2026","journal-title":"IJID One Health"},{"key":"pone.0361136.ref017","doi-asserted-by":"crossref","first-page":"1239079","DOI":"10.3389\/fmicb.2023.1239079","article-title":"Emergence of Marburg virus: A global perspective on fatal outbreaks and clinical challenges","volume":"14","author":"S Srivastava","year":"2023","journal-title":"Front Microbiol"},{"key":"pone.0361136.ref018","doi-asserted-by":"crossref","DOI":"10.1016\/j.nmni.2023.101145","article-title":"Tanzania - The new habitat of Marburg virus","volume":"53","author":"FH Kaifa","year":"2023","journal-title":"New Microbes and New Infections"},{"issue":"7","key":"pone.0361136.ref019","doi-asserted-by":"crossref","DOI":"10.1128\/jvi.00155-24","article-title":"Macaque antibodies targeting Marburg virus glycoprotein induced by multivalent immunization","volume":"98","author":"BM Janus","year":"2024","journal-title":"J Virol"},{"issue":"17","key":"pone.0361136.ref020","doi-asserted-by":"crossref","DOI":"10.1172\/JCI194586","article-title":"Marburg virus glycoprotein mRNA vaccine is more protective than a virus-like particle-forming mRNA vaccine","volume":"135","author":"C Subramani","year":"2025","journal-title":"J Clin Invest"},{"issue":"9","key":"pone.0361136.ref021","doi-asserted-by":"crossref","first-page":"4309","DOI":"10.1128\/JVI.02575-10","article-title":"Marburg virus VP40 antagonizes interferon signaling in a species-specific manner","volume":"85","author":"C Valmas","year":"2011","journal-title":"J Virol"},{"issue":"50","key":"pone.0361136.ref022","doi-asserted-by":"crossref","first-page":"20661","DOI":"10.1073\/pnas.1213559109","article-title":"Structural basis for Marburg virus VP35-mediated immune evasion mechanisms","volume":"109","author":"P Ramanan","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"9977","key":"pone.0361136.ref023","doi-asserted-by":"crossref","first-page":"1545","DOI":"10.1016\/S0140-6736(14)62385-0","article-title":"Safety and immunogenicity of Ebola virus and Marburg virus glycoprotein DNA vaccines assessed separately and concomitantly in healthy Ugandan adults: A phase 1b, randomised, double-blind, placebo-controlled clinical trial","volume":"385","author":"H Kibuuka","year":"2015","journal-title":"Lancet"},{"key":"pone.0361136.ref024","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/s41434-020-00204-y","article-title":"Self-amplifying RNA vaccines for infectious diseases","volume":"28","author":"K Bloom","year":"2021","journal-title":"Gene Ther"},{"key":"pone.0361136.ref025","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1016\/j.jconrel.2021.08.029","article-title":"Polymeric and lipid nanoparticles for delivery of self-amplifying RNA vaccines","volume":"338","author":"AK Blakney","year":"2021","journal-title":"J Control Release"},{"issue":"1","key":"pone.0361136.ref026","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1038\/s41541-025-01302-x","article-title":"Establishing long-lasting vaccine immunity: Insights from mRNA and adjuvanted protein platforms","volume":"10","author":"A-C Pineda-Pe\u00f1a","year":"2025","journal-title":"NPJ Vaccines"},{"issue":"6","key":"pone.0361136.ref027","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.3390\/v14061305","article-title":"A hemagglutinin stem vaccine designed rationally by AlphaFold2 confers broad protection against influenza B infection","volume":"14","author":"D Zeng","year":"2022","journal-title":"Viruses"},{"issue":"2","key":"pone.0361136.ref028","first-page":"3","article-title":"Development of epitope-based vaccine to prevent Marburg virus infection: An in silico approach","author":"SS Thorle","year":"2024","journal-title":"Eureka: LS"},{"key":"pone.0361136.ref029","article-title":"Molecular docking study of sulphonyl hydrazide as an inhibitor of viral protein (VP40) of Marburg virus.","author":"J Muhammad"},{"key":"pone.0361136.ref030","article-title":"Database resources of the National Center for Biotechnology Information","volume":"44","author":"NCBI Resource Coordinators","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"pone.0361136.ref031","article-title":"The Immune Epitope Database (IEDB): 2024 update","volume":"53","author":"IEDB Curation Team Members","year":"2025","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"pone.0361136.ref032","first-page":"160","article-title":"Design of a novel recombinant multi-epitope vaccine against triple-negative breast cancer","volume":"26","author":"H Dariushnejad","year":"2022","journal-title":"Iran Biomed J"},{"key":"pone.0361136.ref033","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/1471-2105-8-238","article-title":"Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method","volume":"8","author":"M Nielsen","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"pone.0361136.ref034","article-title":"Next-generation IEDB tools: A platform for epitope prediction and analysis","volume":"52","author":"Z Yan","year":"2024","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"pone.0361136.ref035","doi-asserted-by":"crossref","first-page":"856","DOI":"10.1016\/j.vaccine.2006.09.032","article-title":"Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties","volume":"25","author":"IA Doytchinova","year":"2007","journal-title":"Vaccine"},{"issue":"6","key":"pone.0361136.ref036","doi-asserted-by":"crossref","first-page":"2278","DOI":"10.1007\/s00894-014-2278-5","article-title":"AllerTOP v.2--a server for in silico prediction of allergens","volume":"20","author":"I Dimitrov","year":"2014","journal-title":"J Mol Model"},{"key":"pone.0361136.ref037","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1007\/978-1-4939-2285-7_7","article-title":"Peptide toxicity prediction","author":"S Gupta","year":"2015","journal-title":"Methods in molecular biology (Clifton, NJ)"},{"key":"pone.0361136.ref038","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1186\/1471-2105-8-361","article-title":"Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines","volume":"8","author":"H-H Bui","year":"2007","journal-title":"BMC Bioinformatics"},{"key":"pone.0361136.ref039","article-title":"UniProt: The universal protein knowledgebase in 2023","volume":"51","author":"A Bateman","year":"2023","journal-title":"Nucleic Acids Research"},{"key":"pone.0361136.ref040","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.meegid.2017.10.022","article-title":"Overlapping CD8+ and CD4+ T-cell epitopes identification for the progression of epitope-based peptide vaccine from nucleocapsid and glycoprotein of emerging Rift Valley fever virus using immunoinformatics approach","volume":"56","author":"UK Adhikari","year":"2017","journal-title":"Infect Genet Evol"},{"key":"pone.0361136.ref041","doi-asserted-by":"crossref","first-page":"6718083","DOI":"10.1155\/2018\/6718083","article-title":"Immunoinformatics approach for epitope-based peptide vaccine design and active site prediction against polyprotein of emerging oropouche virus","volume":"2018","author":"UK Adhikari","year":"2018","journal-title":"J Immunol Res"},{"key":"pone.0361136.ref042","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1186\/1471-2105-7-153","article-title":"Predicting population coverage of T-cell epitope-based diagnostics and vaccines","volume":"7","author":"H-H Bui","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"pone.0361136.ref043","doi-asserted-by":"crossref","first-page":"12420","DOI":"10.1038\/s41598-025-87063-y","article-title":"Immunoinformatics based designing of a multi-epitope cancer vaccine targeting programmed cell death ligand 1","volume":"15","author":"SS Mahafujul","year":"2025","journal-title":"Scientific Reports"},{"issue":"1","key":"pone.0361136.ref044","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1186\/s12865-024-00617-z","article-title":"A novel chimeric vaccine containing multiple epitopes for simulating robust immune activation against Klebsiella pneumoniae","volume":"25","author":"M Hakimian","year":"2024","journal-title":"BMC Immunol"},{"issue":"1","key":"pone.0361136.ref045","doi-asserted-by":"crossref","first-page":"33753","DOI":"10.1038\/s41598-025-99512-9","article-title":"Development of a multi-epitope vaccine against Helicobacter pylori using a novel saRNA technology through an immunoinformatics approach","volume":"15","author":"A Razzak","year":"2025","journal-title":"Sci Rep"},{"key":"pone.0361136.ref046","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1385\/1-59259-890-0:571","article-title":"Protein Identification and Analysis Tools on the ExPASy Server","author":"E Gasteiger","year":"2005","journal-title":"The Proteomics Protocols Handbook"},{"issue":"17","key":"pone.0361136.ref047","doi-asserted-by":"crossref","first-page":"2200","DOI":"10.1093\/bioinformatics\/btp386","article-title":"SOLpro: Accurate sequence-based prediction of protein solubility","volume":"25","author":"CN Magnan","year":"2009","journal-title":"Bioinformatics"},{"issue":"19","key":"pone.0361136.ref048","doi-asserted-by":"crossref","first-page":"3098","DOI":"10.1093\/bioinformatics\/btx345","article-title":"Protein-Sol: A web tool for predicting protein solubility from sequence","volume":"33","author":"M Hebditch","year":"2017","journal-title":"Bioinformatics"},{"issue":"24","key":"pone.0361136.ref049","doi-asserted-by":"crossref","first-page":"3991","DOI":"10.1093\/bioinformatics\/btx521","article-title":"ALIGNSEC: Viewing protein secondary structure predictions within large multiple sequence alignments","volume":"33","author":"G Del\u00e9age","year":"2017","journal-title":"Bioinformatics"},{"issue":"6","key":"pone.0361136.ref050","first-page":"681","article-title":"SOPMA: Significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments","volume":"11","author":"C Geourjon","year":"1995","journal-title":"Comput Appl Biosci"},{"issue":"2","key":"pone.0361136.ref051","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1006\/jmbi.1999.3091","article-title":"Protein secondary structure prediction based on position-specific scoring matrices","volume":"292","author":"DT Jones","year":"1999","journal-title":"J Mol Biol"},{"issue":"6","key":"pone.0361136.ref052","doi-asserted-by":"crossref","first-page":"770","DOI":"10.3390\/brainsci12060770","article-title":"Homology modelling, molecular docking and molecular dynamics simulation studies of CALMH1 against secondary metabolites of bauhinia variegata to treat Alzheimer\u2019s disease","volume":"12","author":"N Khare","year":"2022","journal-title":"Brain Sci"},{"issue":"1","key":"pone.0361136.ref053","first-page":"12","article-title":"RSAD2: An exclusive target protein for Zika virus comparative modeling, characterization, energy minimization and stabilization","volume":"17","author":"PT Rangisetty","year":"2023","journal-title":"Int J Health Sci (Qassim)"},{"issue":"1","key":"pone.0361136.ref054","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/s12860-023-00484-3","article-title":"A computational peptide model induces cancer cells\u2019 apoptosis by docking Kringle 5 to GRP78","volume":"24","author":"I Khater","year":"2023","journal-title":"BMC Mol Cell Biol"},{"issue":"4","key":"pone.0361136.ref055","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nprot.2010.5","article-title":"I-TASSER: A unified platform for automated protein structure and function prediction","volume":"5","author":"A Roy","year":"2010","journal-title":"Nat Protoc"},{"issue":"2","key":"pone.0361136.ref056","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1016\/j.febslet.2013.11.024","article-title":"Protein disulfide engineering","volume":"588","author":"AA Dombkowski","year":"2014","journal-title":"FEBS Lett"},{"key":"pone.0361136.ref057","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1186\/1471-2105-14-346","article-title":"Disulfide by Design 2.0: A web-based tool for disulfide engineering in proteins","volume":"14","author":"DB Craig","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"pone.0361136.ref058","article-title":"GalaxyWEB server for protein structure prediction and refinement","volume":"40","author":"J Ko","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"pone.0361136.ref059","doi-asserted-by":"crossref","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":"M Wiederstein","year":"2007","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"pone.0361136.ref060","doi-asserted-by":"crossref","first-page":"1511","DOI":"10.1002\/pro.5560020916","article-title":"Verification of protein structures: Patterns of nonbonded atomic interactions","volume":"2","author":"C Colovos","year":"1993","journal-title":"Protein Sci"},{"issue":"2","key":"pone.0361136.ref061","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1107\/S1600576725001669","article-title":"RamPlot: A webserver to draw 2D, 3D and assorted Ramachandran (\u03c6, \u03c8) maps","volume":"58","author":"M Kumar","year":"2025","journal-title":"J Appl Crystallogr"},{"key":"pone.0361136.ref062","doi-asserted-by":"crossref","first-page":"101422","DOI":"10.1016\/j.imu.2023.101422","article-title":"Designing of a multiepitope-based chimeric vaccine against dengue virus serotype 3 (DENV-3) through next generation reverse vaccinology approaches","volume":"44","author":"MHU Masum","year":"2024","journal-title":"Informatics in Medicine Unlocked"},{"issue":"9","key":"pone.0361136.ref063","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0310398","article-title":"Designing of a chimeric multiepitope vaccine against bancroftian lymphatic filariasis through immunoinformatics approaches","volume":"19","author":"R Parvin","year":"2024","journal-title":"PLoS One"},{"key":"pone.0361136.ref064","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1186\/1471-2105-9-514","article-title":"ElliPro: A new structure-based tool for the prediction of antibody epitopes","volume":"9","author":"J Ponomarenko","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"pone.0361136.ref065","doi-asserted-by":"crossref","first-page":"983","DOI":"10.3390\/biom14080983","article-title":"Computational methods to predict conformational b-cell epitopes","volume":"14","author":"M Carroll","year":"2024","journal-title":"Biomolecules"},{"key":"pone.0361136.ref066","doi-asserted-by":"crossref","first-page":"1227833","DOI":"10.3389\/fimmu.2023.1227833","article-title":"Application of toll-like receptors (TLRs) and their agonists in cancer vaccines and immunotherapy","volume":"14","author":"S Chakraborty","year":"2023","journal-title":"Front Immunol"},{"key":"pone.0361136.ref067","doi-asserted-by":"crossref","first-page":"102172","DOI":"10.1016\/j.cbpa.2022.102172","article-title":"Toll-like receptor (TLR) agonists as a driving force behind next-generation vaccine adjuvants and cancer therapeutics","volume":"70","author":"A Kaur","year":"2022","journal-title":"Curr Opin Chem Biol"},{"issue":"1","key":"pone.0361136.ref068","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1093\/nar\/28.1.235","article-title":"The Protein Data Bank","volume":"28","author":"HM Berman","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"pone.0361136.ref069","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1107\/S2059798322002741","article-title":"Elucidation of protein function using computational docking and hotspot analysis by ClusPro and FTMap","volume":"78","author":"G Jones","year":"2022","journal-title":"Acta Crystallogr D Struct Biol"},{"issue":"2","key":"pone.0361136.ref070","doi-asserted-by":"crossref","DOI":"10.1002\/wcms.1298","article-title":"Using PyMOL as a platform for computational drug design","volume":"7","author":"S Yuan","year":"2017","journal-title":"WIREs Comput Mol Sci"},{"issue":"12","key":"pone.0361136.ref071","doi-asserted-by":"crossref","first-page":"488","DOI":"10.1016\/S0968-0004(97)01140-7","article-title":"PDBsum: A Web-based database of summaries and analyses of all PDB structures","volume":"22","author":"RA Laskowski","year":"1997","journal-title":"Trends Biochem Sci"},{"key":"pone.0361136.ref072","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1007\/978-1-0716-1855-4_13","article-title":"Structural prediction of peptide-MHC binding modes","volume":"2405","author":"MAS Perez","year":"2022","journal-title":"Methods Mol Biol"},{"issue":"10","key":"pone.0361136.ref073","doi-asserted-by":"crossref","first-page":"1620","DOI":"10.3390\/vaccines11101620","article-title":"In silico analyses, experimental verification and application in DNA vaccines of ebolavirus GP-Derived pan-MHC-II-restricted epitopes","volume":"11","author":"J Zhang","year":"2023","journal-title":"Vaccines (Basel)"},{"issue":"2","key":"pone.0361136.ref074","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/nmeth.1818","article-title":"HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment","volume":"9","author":"M Remmert","year":"2011","journal-title":"Nat Methods"},{"issue":"49","key":"pone.0361136.ref075","doi-asserted-by":"crossref","first-page":"12027","DOI":"10.1021\/acs.jpcb.4c06614","article-title":"Editorial guidelines for computational studies of ligand binding using MM\/PBSA and MM\/GBSA approximations wisely","volume":"128","author":"B Roux","year":"2024","journal-title":"J Phys Chem B"},{"issue":"1","key":"pone.0361136.ref076","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1021\/ci100275a","article-title":"Assessing the performance of the MM\/PBSA and MM\/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations","volume":"51","author":"T Hou","year":"2011","journal-title":"J Chem Inf Model"},{"issue":"1","key":"pone.0361136.ref077","doi-asserted-by":"crossref","first-page":"13954","DOI":"10.1038\/s41598-025-96989-2","article-title":"Computational design of a glycosylated multi-epitope vaccine against HAsV-1 and HAsV-2 astrovirus for acute gastroenteritis","volume":"15","author":"M Naveed","year":"2025","journal-title":"Sci Rep"},{"key":"pone.0361136.ref078","article-title":"Designing a multi-epitope vaccine against HPV 16, 18, 33, and 45 targeting L1 and E7 proteins: An immunoinformatics approach for cervical cancer prevention and therapy","volume":"19","author":"MTT Tusar","year":"2025","journal-title":"Bioinformatics and Biology Insights"},{"key":"pone.0361136.ref079","doi-asserted-by":"crossref","DOI":"10.1177\/11779322241264145","article-title":"Antiviral activity, pharmacoinformatics, molecular docking, and dynamics studies of Azadirachta indica against Nipah virus by targeting envelope glycoprotein: emerging strategies for developing antiviral treatment","volume":"18","author":"O Saha","year":"2024","journal-title":"Bioinformatics and Biology Insights"},{"key":"pone.0361136.ref080","doi-asserted-by":"crossref","first-page":"101458","DOI":"10.1016\/j.imu.2024.101458","article-title":"In-silico identification of novel natural drug leads against the Ebola virus VP40 protein: A promising approach for developing new antiviral therapeutics","volume":"45","author":"NH Siddiquee","year":"2024","journal-title":"Informatics in Medicine Unlocked"},{"key":"pone.0361136.ref081","doi-asserted-by":"crossref","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":"A Grote","year":"2005","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pone.0361136.ref082","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1186\/s40478-022-01356-1","article-title":"The amyloid plaque proteome in early onset Alzheimer\u2019s disease and Down syndrome","volume":"10","author":"E Drummond","year":"2022","journal-title":"Acta Neuropathol Commun"},{"issue":"4","key":"pone.0361136.ref083","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0009862","article-title":"Computational immunology meets bioinformatics: The use of prediction tools for molecular binding in the simulation of the immune system","volume":"5","author":"N Rapin","year":"2010","journal-title":"PLoS One"},{"issue":"14","key":"pone.0361136.ref084","doi-asserted-by":"crossref","first-page":"2013","DOI":"10.1093\/bioinformatics\/btr335","article-title":"Immune system simulation online","volume":"27","author":"N Rapin","year":"2011","journal-title":"Bioinformatics"},{"key":"pone.0361136.ref085","doi-asserted-by":"crossref","first-page":"11779322251331104","DOI":"10.1177\/11779322251331104","article-title":"A reverse vaccinology and immunoinformatic approach for the designing of a novel mRNA vaccine against stomach cancer targeting the potent pathogenic proteins of Helicobacter pylori","volume":"19","author":"A Barua","year":"2025","journal-title":"Bioinform Biol Insights"},{"key":"pone.0361136.ref086","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkn188","article-title":"The Vienna RNA websuite","volume":"36","author":"AR Gruber","year":"2008","journal-title":"Nucleic Acids Res"},{"key":"pone.0361136.ref087","article-title":"Revolutionizing chikungunya vaccines: mRNA breakthroughs with molecular and immune simulations","volume":"19","author":"MHU Masum","year":"2025","journal-title":"Bioinformatics and Biology Insights"},{"key":"pone.0361136.ref088","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/s12859-016-0918-8","article-title":"Design, structure prediction and molecular dynamics simulation of a fusion construct containing malaria pre-erythrocytic vaccine candidate, PfCelTOS, and human interleukin 2 as adjuvant","volume":"17","author":"S Shamriz","year":"2016","journal-title":"BMC Bioinformatics"},{"key":"pone.0361136.ref089","article-title":"Pathogenesis of Marburg hemorrhagic fever in cynomolgus macaques","author":"LE Hensley","year":"2011","journal-title":"J Infect Dis"},{"issue":"6","key":"pone.0361136.ref090","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.01865-18","article-title":"A Recombinant rabies virus expressing the marburg virus glycoprotein is dependent upon antibody-mediated cellular cytotoxicity for protection against marburg virus disease in a murine model","volume":"93","author":"R Keshwara","year":"2019","journal-title":"J Virol"},{"issue":"10373","key":"pone.0361136.ref091","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1016\/S0140-6736(22)02400-X","article-title":"Safety, tolerability, and immunogenicity of the chimpanzee adenovirus type 3-vectored Marburg virus (cAd3-Marburg) vaccine in healthy adults in the USA: A first-in-human, phase 1, open-label, dose-escalation trial","volume":"401","author":"MJ Hamer","year":"2023","journal-title":"Lancet"},{"key":"pone.0361136.ref092","first-page":"433","article-title":"Individual success is not liberation: A critique of #girlboss and neoliberal feminisms","volume":"47","author":"A Ara\u00fajo","year":"2024","journal-title":"CONCEPT"},{"issue":"10","key":"pone.0361136.ref093","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1010805","article-title":"An introduction to the Marburg virus vaccine consortium, MARVAC","volume":"18","author":"RW Cross","year":"2022","journal-title":"PLoS Pathog"},{"issue":"2","key":"pone.0361136.ref094","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1016\/j.vaccine.2020.11.042","article-title":"Systematic review of Marburg virus vaccine nonhuman primate studies and human clinical trials","volume":"39","author":"N Dulin","year":"2021","journal-title":"Vaccine"},{"issue":"1","key":"pone.0361136.ref095","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1186\/s43141-023-00575-w","article-title":"Designing a novel and combinatorial multi-antigenic epitope-based vaccine \u201cMarVax\u201d against Marburg virus-a reverse vaccinology and immunoinformatics approach","volume":"21","author":"B Debroy","year":"2023","journal-title":"J Genet Eng Biotechnol"},{"issue":"47","key":"pone.0361136.ref096","doi-asserted-by":"crossref","first-page":"32043","DOI":"10.1021\/acsomega.1c04817","article-title":"Designing of a multi-epitope vaccine against the structural proteins of marburg virus exploiting the immunoinformatics approach","volume":"6","author":"SA Sami","year":"2021","journal-title":"ACS Omega"},{"key":"pone.0361136.ref097","doi-asserted-by":"crossref","first-page":"907481","DOI":"10.3389\/fimmu.2022.907481","article-title":"Mining of marburg virus proteome for designing an epitope-based vaccine","volume":"13","author":"MA Soltan","year":"2022","journal-title":"Front Immunol"},{"issue":"1","key":"pone.0361136.ref098","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s12896-024-00873-2","article-title":"Design of a novel multi-epitope vaccine against Marburg virus using immunoinformatics studies","volume":"24","author":"FQJ Al-Zayadi","year":"2024","journal-title":"BMC Biotechnol"},{"issue":"4","key":"pone.0361136.ref099","doi-asserted-by":"crossref","first-page":"566","DOI":"10.3390\/v17040566","article-title":"Self-amplifying RNA: Advantages and challenges of a versatile platform for vaccine development","volume":"17","author":"T Vallet","year":"2025","journal-title":"Viruses"},{"key":"pone.0361136.ref100","doi-asserted-by":"crossref","first-page":"5560605","DOI":"10.1155\/2023\/5560605","article-title":"Computational modeling and evaluation of potential mRNA and peptide-based vaccine against Marburg virus (MARV) to provide immune protection against hemorrhagic fever","volume":"2023","author":"FF Albaqami","year":"2023","journal-title":"BioMed Research International"},{"issue":"7","key":"pone.0361136.ref101","article-title":"An mRNA vaccine for pancreatic cancer designed by applying in silico immunoinformatics and reverse vaccinology approaches","volume":"19","author":"MHU Masum","year":"2024","journal-title":"PLoS One"},{"key":"pone.0361136.ref102","doi-asserted-by":"crossref","DOI":"10.1016\/j.csbr.2025.100049","article-title":"Next-gen vaccine design: Integrating proteomics and bioinformatics for japanese encephalitis","volume":"2","author":"AA Mahdeen","year":"2025","journal-title":"Comput Struct Biotechnol Rep"},{"issue":"47","key":"pone.0361136.ref103","doi-asserted-by":"crossref","first-page":"32043","DOI":"10.1021\/acsomega.1c04817","article-title":"Designing of a multi-epitope vaccine against the structural proteins of marburg virus exploiting the immunoinformatics approach","volume":"6","author":"SA Sami","year":"2021","journal-title":"ACS Omega"},{"key":"pone.0361136.ref104","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1016\/bs.apcsb.2021.01.007","article-title":"The concept of protein folding\/unfolding and its impacts on human health","volume":"126","author":"L Alaei","year":"2021","journal-title":"Adv Protein Chem Struct Biol"},{"key":"pone.0361136.ref105","first-page":"3502514","article-title":"Insights into the molecular mechanisms of protein-ligand interactions by molecular docking and molecular dynamics simulation: A case of oligopeptide binding protein","volume":"2018","author":"Y Fu","year":"2018","journal-title":"Comput Math Methods Med"},{"key":"pone.0361136.ref106","doi-asserted-by":"crossref","first-page":"1129","DOI":"10.1016\/j.neuron.2018.08.011","article-title":"Molecular dynamics simulation for all","volume":"99","author":"SA Hollingsworth","year":"2018","journal-title":"Neuron"},{"issue":"6","key":"pone.0361136.ref107","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.3390\/biomedicines13061439","article-title":"Design and Validation of a Multi-Epitope mRNA Vaccine Construct Against Human Monkeypox Virus (hMPXV) by Annotating Protein of Intracellular Mature Virus (IMV) Form of hMPXV","volume":"13","author":"MA Izhari","year":"2025","journal-title":"Biomedicines"},{"issue":"6","key":"pone.0361136.ref108","doi-asserted-by":"crossref","first-page":"547","DOI":"10.1021\/acsmeasuresciau.2c00048","article-title":"Measuring the radius of gyration and intrinsic flexibility of viral proteins in buffer solution using small-angle X-ray scattering","volume":"2","author":"R Funari","year":"2022","journal-title":"ACS Meas Sci Au"},{"key":"pone.0361136.ref109","doi-asserted-by":"crossref","first-page":"1042997","DOI":"10.3389\/fimmu.2022.1042997","article-title":"Immunoinformatic-based design of immune-boosting multiepitope subunit vaccines against monkeypox virus and validation through molecular dynamics and immune simulation","volume":"13","author":"M Suleman","year":"2022","journal-title":"Front Immunol"},{"issue":"7","key":"pone.0361136.ref110","article-title":"RNA secondary structure analysis using RNAstructure","volume":"3","author":"SE Ali","year":"2023","journal-title":"Curr Protoc"}],"container-title":["PLOS One"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0361136","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T17:26:55Z","timestamp":1792776415000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0361136"}},"subtitle":[],"editor":[{"given":"Mohammad","family":"Faezi Ghasemi","sequence":"first","affiliation":[{"name":"Islamic Azad University","place":["IRAN, ISLAMIC REPUBLIC OF"]}],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2026,10,23]]},"references-count":110,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2026,10,23]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0361136","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,23]]}}}