{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T05:01:23Z","timestamp":1785214883945,"version":"3.55.0"},"reference-count":74,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2022,6,1]],"date-time":"2022-06-01T00:00:00Z","timestamp":1654041600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Vaccines"],"abstract":"<jats:p>Enterobacter cloacae (EC) is a significant emerging pathogen that is occasionally associated with lung infection, surgical site infection, urinary infection, sepsis, and outbreaks in neonatal intensive care units. In light of the fact that there is currently no approved vaccine or therapeutic option for the treatment of EC, the current study was developed to concentrate on applications based on modern computational approaches to design a multi-epitope-based E. cloacae peptide vaccine (MEBEPV) expressing the antigenic determinants prioritized from the EC genome. Integrated computational analyses identified two potential protein targets (phosphoporin protein-PhoE and putative outer-membrane porin protein) for further exploration on the basis of pangenome subtractive proteomics and immunoinformatic in-depth examination of the core proteomes. Then, a multi-epitope peptide vaccine was designed, which comprised shortlisted epitopes that were capable of eliciting both innate and adaptive immunity, as well as the cholera toxin\u2019s B-subunit, which was used as an adjuvant in the vaccine formulation. To ensure maximum expression, the vaccine\u2019s 3D structure was developed and the loop was refined, improving the stability by disulfide engineering, and the physicochemical characteristics of the recombinant vaccine sequence were found to be ideal for both in vitro and in vivo experimentation. Blind docking was then used for the prediction of the MEBEPV predominant blinding mode with MHCI, MHCII, and TLR3 innate immune receptors, with lowest global energy of \u221218.64 kJ\/mol, \u221248.25 kJ\/mol, and \u22125.20 kJ\/mol for MHC-I, MHC-II, and TLR-4, respectively, with docked complexes considered for simulation. In MD and MMGBSA investigations, the docked models of MEBEPV-TLR3, MEBEPV-MHCI, and MEBEPV-MHCII were found to be stable during the course of the simulation. MM-GBSA analysis calculated \u2212122.17 total net binding free energies for the TLR3-vaccine complex, \u2212125.4 for the MHC I-vaccine complex, and \u2212187.94 for the MHC II-vaccine complex. Next, MM-PBSA analysis calculated \u2212115.63 binding free energy for the TLR3-vaccine complex, \u2212118.19 for the MHC I-vaccine complex, and \u2212184.61 for the MHC II-vaccine complex. When the vaccine was tested in silico, researchers discovered that it was capable of inducing both types of immune responses (cell mediated and humoral) at the same time. Even though the suggested MEBEPV has the potential to be a powerful contender against E. cloacae-associated illnesses, further testing in the laboratory will be required before it can be declared safe and immunogenic.<\/jats:p>","DOI":"10.3390\/vaccines10060886","type":"journal-article","created":{"date-parts":[[2022,6,1]],"date-time":"2022-06-01T21:43:42Z","timestamp":1654119822000},"page":"886","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Design of a Multi-Epitopes Based Chimeric Vaccine against Enterobacter cloacae Using Pan-Genome and Reverse Vaccinology Approaches"],"prefix":"10.3390","volume":"10","author":[{"given":"Wafa Abdullah I.","family":"Al-Megrin","sequence":"first","affiliation":[{"name":"Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alaa","family":"Karkashan","sequence":"additional","affiliation":[{"name":"Department of Biology, College of Sciences, University of Jeddah, Jeddah 21959, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9306-609X","authenticated-orcid":false,"given":"Abdullah M.","family":"Alnuqaydan","sequence":"additional","affiliation":[{"name":"Department of Medical Biotechnology, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faris F.","family":"Aba Alkhayl","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia"},{"name":"Department of Pharmaceutical Chemistry and Pharmacognosy, College of Dentistry and Pharmacy, Buraydah Colleges, Buraydah 51418, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0850-5500","authenticated-orcid":false,"given":"Faris","family":"Alrumaihi","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1491-6402","authenticated-orcid":false,"given":"Ahmad","family":"Almatroudi","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6486-9835","authenticated-orcid":false,"given":"Khaled S.","family":"Allemailem","sequence":"additional","affiliation":[{"name":"Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2022,6,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.tifs.2018.08.001","article-title":"Antibiotic resistance in foodborne bacteria","volume":"84","author":"Manageiro","year":"2019","journal-title":"Trends Food Sci. Technol."},{"key":"ref_2","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_3","doi-asserted-by":"crossref","first-page":"1082","DOI":"10.1126\/science.aax3879","article-title":"The evolution of antibiotic resistance","volume":"365","author":"MacLean","year":"2019","journal-title":"Science"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"5568","DOI":"10.3390\/ijerph19095568","article-title":"Vaccinomics to Design a Multi-Epitopes Vaccine for Acinetobacter baumannii","volume":"19","author":"Albutti","year":"2022","journal-title":"Int. J. Environ. Res. Public Health"},{"key":"ref_5","first-page":"344","article-title":"The antibiotic resistance crisis: Part 2: Management strategies and new agents","volume":"40","author":"Ventola","year":"2015","journal-title":"Pharm. Ther."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"105258","DOI":"10.1016\/j.ejps.2020.105258","article-title":"Vaccinomics to design a novel single chimeric subunit vaccine for broad-spectrum immunological applications targeting nosocomial Enterobacteriaceae pathogens","volume":"146","author":"Ismail","year":"2020","journal-title":"Eur. J. Pharm. Sci."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/j.molcel.2014.03.010","article-title":"Bacteria fighting back: How pathogens target and subvert the host innate immune system","volume":"54","author":"Reddick","year":"2014","journal-title":"Molecular Cell"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1016\/j.idc.2016.02.001","article-title":"Overview: Global and local impact of antibiotic resistance","volume":"30","author":"Watkins","year":"2016","journal-title":"Infect. Dis. Clin. N. Am."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1080\/14760584.2018.1470507","article-title":"Vaccines for healthcare-associated infections: Present, future, and expectations","volume":"17","author":"Lucht","year":"2018","journal-title":"Expert Rev. Vaccines"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1787","DOI":"10.1128\/JCM.42.4.1787-1789.2004","article-title":"Multiplex PCR for diagnosis of enteric infections associated with diarrheagenic Escherichia coli","volume":"42","author":"Vidal","year":"2004","journal-title":"J. Clin. Microbiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1016\/j.immuni.2010.09.017","article-title":"Reverse vaccinology: Developing vaccines in the era of genomics","volume":"33","author":"Sette","year":"2010","journal-title":"Immunity"},{"key":"ref_12","unstructured":"Okafor, C.N., and Momodu, I.I. (2022, April 13). Bacillus Calmette Guerin (BCG). Available online: https:\/\/europepmc.org\/article\/med\/30844212."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.ejca.2019.01.021","article-title":"Oncologic and fertility impact of surgical approach for borderline ovarian tumours treated with fertility sparing surgery","volume":"111","author":"Ceppi","year":"2019","journal-title":"Eur. J. Cancer"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1016\/j.drudis.2008.12.007","article-title":"The use of genomics in microbial vaccine development","volume":"14","author":"Bambini","year":"2009","journal-title":"Drug Discov. Today"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2315","DOI":"10.3389\/fimmu.2018.02315","article-title":"Bacterial vaccine antigen discovery in the reverse vaccinology 2.0 Era: Progress and challenges","volume":"9","author":"Bidmos","year":"2018","journal-title":"Front. Immunol."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Schneider, L.S., Olin, J.T., Doody, R.S., Clark, C.M., Morris, J.C., Reisberg, B., Ferris, S.H., Schmitt, F.A., Grundman, M., and Thomas, R.G. (1997). Validity and reliability of the Alzheimer\u2019s Disease Cooperative Study-Clinical global impression of change (ADCS-CGIC). Alzheimer Disease, Springer.","DOI":"10.1037\/t44222-000"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1016\/0264-410X(94)00037-N","article-title":"Efficacy, safety, and immunogenicity of a meningococcal group B (15: P1. 3) outer membrane protein vaccine in Iquique, Chile","volume":"13","author":"Boslego","year":"1995","journal-title":"Vaccine"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"469","DOI":"10.1084\/jem.20151960","article-title":"Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design","volume":"213","author":"Rappuoli","year":"2016","journal-title":"J. Exp. Med."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/S1359-6446(03)02689-8","article-title":"Reverse vaccinology","volume":"8","author":"Mora","year":"2003","journal-title":"Drug Discov. Today"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Albekairi, T.H., Alshammari, A., Alharbi, M., Alshammary, A.F., Tahir ul Qamar, M., Ullah, A., Irfan, M., and Ahmad, S. (2022). Designing of a Novel Multi-Antigenic Epitope-Based Vaccine against E. hormaechei: An Intergraded Reverse Vaccinology and Immunoinformatics Approach. Vaccines, 10.","DOI":"10.3390\/vaccines10050665"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"963","DOI":"10.1586\/erv.09.67","article-title":"Next-generation sequencing: A transformative tool for vaccinology","volume":"8","author":"Dhiman","year":"2009","journal-title":"Expert Rev. Vaccines"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"113","DOI":"10.3389\/fimmu.2019.00113","article-title":"Comparison of open-source reverse vaccinology programs for bacterial vaccine antigen discovery","volume":"10","author":"Dalsass","year":"2019","journal-title":"Front. Immunol."},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Albekairi, T.H., Alshammari, A., Alharbi, M., Alshammary, A.F., Tahir ul Qamar, M., Anwar, T., Ismail, S., Shaker, B., and Ahmad, S. (2022). Design of a Multi-Epitope Vaccine against Tropheryma whipplei Using Immunoinformatics and Molecular Dynamics Simulation Techniques. Vaccines, 10.","DOI":"10.3390\/vaccines10050691"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1016\/j.mib.2006.07.003","article-title":"Microbial genomes and vaccine design: Refinements to the classical reverse vaccinology approach","volume":"9","author":"Mora","year":"2006","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"105120","DOI":"10.1016\/j.meegid.2021.105120","article-title":"Identification of immunodominant epitopes in allelic variants VK210 and VK247 of Plasmodium Vivax Circumsporozoite immunogen","volume":"96","author":"Naz","year":"2021","journal-title":"Infect. Genet. Evol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"148","DOI":"10.1126\/science.1109869","article-title":"Identification of a universal Group B streptococcus vaccine by multiple genome screen","volume":"309","author":"Maione","year":"2005","journal-title":"Science"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-018-26689-7","article-title":"Subtractive proteomics to identify novel drug targets and reverse vaccinology for the development of chimeric vaccine against Acinetobacter baumannii","volume":"8","author":"Solanki","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1093\/jac\/dkab434","article-title":"Identification of Multiple Transfer Units and Novel Subtypes of TmexCD-ToprJ Gene Clusters in Clinical Carbapenem-Resistant Enterobacter cloacae and Klebsiella oxytoca","volume":"77","author":"Sun","year":"2022","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_29","first-page":"392","article-title":"Enterobacter aerogenes and Enterobacter cloacae; versatile bacterial pathogens confronting antibiotic treatment","volume":"6","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref_30","unstructured":"Fraser, S., Sinave, C., and Mileno, M. (2014). Enterobacter Infections: Practice Essentials, Background, Pathophysiology. Pathophysiology."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1093\/cid\/cix934","article-title":"Genomic investigation of a putative endoscope-associated carbapenem-resistant Enterobacter cloacae outbreak reveals a wide diversity of circulating strains and resistance mutations","volume":"66","author":"Hawken","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Michalik, M., Djahanschiri, B., Leo, J.C., and Linke, D. (2022). An Update on \u201cReverse Vaccinology\u201d: The Pathway from Genomes and Epitope Predictions to Tailored, Recombinant Vaccines. Vaccine Des., 45\u201371.","DOI":"10.1007\/978-1-0716-1892-9_4"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"7123","DOI":"10.1073\/pnas.1423977112","article-title":"Production of extremely low volatile organic compounds from biogenic emissions: Measured yields and atmospheric implications","volume":"112","author":"Jokinen","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1146\/annurev-immunol-032414-112240","article-title":"Innate immune pattern recognition: A cell biological perspective","volume":"33","author":"Brubaker","year":"2015","journal-title":"Annu. Rev. Immunol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-019-40833-x","article-title":"In-silico design of a multi-epitope vaccine candidate against onchocerciasis and related filarial diseases","volume":"9","author":"Shey","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"646","DOI":"10.1038\/nsb0902-646","article-title":"Molecular dynamics simulations of biomolecules","volume":"9","author":"Karplus","year":"2002","journal-title":"Nat. Struct. Biol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2079","DOI":"10.1021\/ci3001919","article-title":"The normal-mode entropy in the MM\/GBSA method: Effect of system truncation, buffer region, and dielectric constant","volume":"52","author":"Genheden","year":"2012","journal-title":"J. Chem. Inf. Modeling"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2463","DOI":"10.1128\/JB.00067-10","article-title":"Complete genome sequence of Enterobacter cloacae subsp. cloacae type strain ATCC 13047","volume":"192","author":"Ren","year":"2010","journal-title":"J. Bacteriol."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"D13","DOI":"10.1093\/nar\/gkm1000","article-title":"Database resources of the National Center for Biotechnology Information","volume":"36","author":"Wheeler","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"234","DOI":"10.6026\/97320630005234","article-title":"Protein sequence redundancy reduction: Comparison of various method","volume":"5","author":"Sikic","year":"2010","journal-title":"Bioinformation"},{"key":"ref_41","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_42","doi-asserted-by":"crossref","first-page":"D325","DOI":"10.1093\/nar\/gki008","article-title":"VFDB: A reference database for bacterial virulence factors","volume":"33","author":"Chen","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1097\/JOM.0000000000002039","article-title":"Impact of heat index and ultraviolet index on COVID-19 in major cities of Pakistan","volume":"63","author":"Adnan","year":"2021","journal-title":"J. Occup. Environ. Med."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"D339","DOI":"10.1093\/nar\/gky1006","article-title":"The immune epitope database (IEDB): 2018 update","volume":"47","author":"Vita","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"55","DOI":"10.2165\/00822942-200605010-00008","article-title":"MHCPred 2.0","volume":"5","author":"Guan","year":"2006","journal-title":"Appl. Bioinform."},{"key":"ref_46","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_47","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1745-6150-8-30","article-title":"Designing of interferon-gamma inducing MHC class-II binders","volume":"8","author":"Dhanda","year":"2013","journal-title":"Biol. Direct"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"74","DOI":"10.6026\/97320630012074","article-title":"MFPPI\u2013multi FASTA ProtParam interface","volume":"12","author":"Garg","year":"2016","journal-title":"Bioinformation"},{"key":"ref_49","unstructured":"Dimitrov, I., Flower, D.R., and Doytchinova, I. (2011, January 18\u201321). AllerTOP-a server for in silico prediction of allergens. Proceedings of the BMC Bioinformatics, 10th International Conference on Artificial Immune Systems (ICARIS), Cambraige, UK."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"W294","DOI":"10.1093\/nar\/gks493","article-title":"GalaxyWEB server for protein structure prediction and refinement","volume":"40","author":"Ko","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"ref_51","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_52","doi-asserted-by":"crossref","first-page":"2230","DOI":"10.1007\/s00259-017-3799-9","article-title":"TSPO PET for glioma imaging using the novel ligand 18F-GE-180: First results in patients with glioblastoma","volume":"44","author":"Albert","year":"2017","journal-title":"Eur. J. Nucl. Med. Mol. Imaging"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"2013","DOI":"10.1093\/bioinformatics\/btr335","article-title":"Immune system simulation online","volume":"27","author":"Rapin","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"W363","DOI":"10.1093\/nar\/gki481","article-title":"PatchDock and SymmDock: Servers for rigid and symmetric docking","volume":"33","author":"Inbar","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1002\/prot.21495","article-title":"FireDock: Fast interaction refinement in molecular docking","volume":"69","author":"Andrusier","year":"2007","journal-title":"Proteins Struct. Funct. Bioinform."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.1002\/jcc.20084","article-title":"UCSF Chimera\u2014A visualization system for exploratory research and analysis","volume":"25","author":"Pettersen","year":"2004","journal-title":"J. Comput. Chem."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"2090","DOI":"10.1063\/1.1332996","article-title":"Langevin stabilization of molecular dynamics","volume":"114","author":"Izaguirre","year":"2001","journal-title":"J. Chem. Phys."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1002\/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V","article-title":"A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations","volume":"22","year":"2001","journal-title":"J. Comput. Chem."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1080\/00268977200100031","article-title":"NpT-ensemble Monte Carlo calculations for binary liquid mixtures","volume":"23","author":"McDonald","year":"1972","journal-title":"Mol. Phys."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: Visual molecular dynamics","volume":"14","author":"Humphrey","year":"1996","journal-title":"J. Mol. Graph."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"3314","DOI":"10.1021\/ct300418h","article-title":"MMPBSA. py: An efficient program for end-state free energy calculations","volume":"8","author":"Miller","year":"2012","journal-title":"J. Chem. Theory Comput."},{"key":"ref_62","unstructured":"Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., and Walter, P. (2002). Helper T cells and lymphocyte activation. Molecular Biology of the Cell, Garland Science. [4th ed.]."},{"key":"ref_63","unstructured":"Travers, P., Walport, M., Shlomchik, M.J., and Janeway, M. (1997). Immunobiology: The Immune System in Health and Disease, Churchill Livingstone."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"105160","DOI":"10.1016\/j.ejps.2019.105160","article-title":"Immunoinformatics design of a novel multi-epitope peptide vaccine to combat multi-drug resistant infections caused by Vibrio vulnificus","volume":"142","author":"Abbas","year":"2020","journal-title":"Eur. J. Pharm. Sci."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"105151","DOI":"10.1016\/j.compbiomed.2021.105151","article-title":"Designing of a multi-epitopes-based peptide vaccine against rift valley fever virus and its validation through integrated computational approaches","volume":"141","author":"Fatima","year":"2022","journal-title":"Comput. Biol. Med."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Ullah, A., Ahmad, S., Ismail, S., Afsheen, Z., Khurram, M., Tahir ul Qamar, M., AlSuhaymi, N., Alsugoor, M.H., and Allemailem, K.S. (2021). Towards A Novel Multi-Epitopes Chimeric Vaccine for Simulating Strong Immune Responses and Protection against Morganella morganii. Int. J. Environ. Res. Public Health, 18.","DOI":"10.3390\/ijerph182010961"},{"key":"ref_67","doi-asserted-by":"crossref","unstructured":"Aslam, S., Ahmad, S., Noor, F., Ashfaq, U.A., Shahid, F., Rehman, A., Tahir ul Qamar, M., Alatawi, E.A., Alshabrmi, F.M., and Allemailem, K.S. (2021). Designing a Multi-Epitope Vaccine against Chlamydia trachomatis by Employing Integrated Core Proteomics, Immuno-Informatics and In Silico Approaches. Biology, 10.","DOI":"10.3390\/biology10100997"},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"104389","DOI":"10.1016\/j.compbiomed.2021.104389","article-title":"Designing multi-epitope vaccine against Staphylococcus aureus by employing subtractive proteomics, reverse vaccinology and immuno-informatics approaches","volume":"132","author":"Ahmad","year":"2021","journal-title":"Comput. Biol. Med."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"11197","DOI":"10.1038\/s41598-021-90868-2","article-title":"Designing a multi-epitope vaccine against Mycobacteroides abscessus by pangenome-reverse vaccinology","volume":"11","author":"Dar","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"669812","DOI":"10.3389\/fimmu.2021.669812","article-title":"Development of a novel multi-epitope vaccine against crimean-congo hemorrhagic fever virus: An integrated reverse vaccinology, vaccine informatics and biophysics approach","volume":"12","author":"Qamar","year":"2021","journal-title":"Front. Immunol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"278","DOI":"10.3389\/fimmu.2017.00278","article-title":"The immune epitope database and analysis resource in epitope discovery and synthetic vaccine design","volume":"8","author":"Fleri","year":"2017","journal-title":"Front. Immunol."},{"key":"ref_72","doi-asserted-by":"crossref","unstructured":"Rehman, A., Ahmad, S., Shahid, F., Albutti, A., Alwashmi, A.S., Aljasir, M.A., Alhumeed, N., Qasim, M., Ashfaq, U.A., and Tahir ul Qamar, M. (2021). Integrated Core Proteomics, Subtractive Proteomics, and Immunoinformatics Investigation to Unveil a Potential Multi-Epitope Vaccine against Schistosomiasis. Vaccines, 9.","DOI":"10.3390\/vaccines9060658"},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Potocnakova, L., Bhide, M., and Pulzova, L.B. (2016). An introduction to B-cell epitope mapping and in silico epitope prediction. J. Immunol. Res., 2016.","DOI":"10.1155\/2016\/6760830"},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"104705","DOI":"10.1016\/j.compbiomed.2021.104705","article-title":"Pan-vaccinomics approach towards a universal vaccine candidate against WHO priority pathogens to address growing global antibiotic resistance","volume":"136","author":"Ismail","year":"2021","journal-title":"Comput. Biol. Med."}],"container-title":["Vaccines"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-393X\/10\/6\/886\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T23:23:17Z","timestamp":1760138597000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-393X\/10\/6\/886"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,1]]},"references-count":74,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2022,6]]}},"alternative-id":["vaccines10060886"],"URL":"https:\/\/doi.org\/10.3390\/vaccines10060886","relation":{},"ISSN":["2076-393X"],"issn-type":[{"value":"2076-393X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,6,1]]}}}