{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T20:21:28Z","timestamp":1790281288093,"version":"4.1.0"},"reference-count":95,"publisher":"MDPI AG","issue":"20","license":[{"start":{"date-parts":[[2021,10,19]],"date-time":"2021-10-19T00:00:00Z","timestamp":1634601600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJERPH"],"abstract":"<jats:p>Morganella morganii is one of the main etiological agents of hospital-acquired infections and no licensed vaccine is available against the pathogen. Herein, we designed a multi-epitope-based vaccine against M. morganii. Predicted proteins from fully sequenced genomes of the pathogen were subjected to a core sequences analysis, followed by the prioritization of non-redundant, host non-homologous and extracellular, outer membrane and periplasmic membrane virulent proteins as vaccine targets. Five proteins (TonB-dependent siderophore receptor, serralysin family metalloprotease, type 1 fimbrial protein, flagellar hook protein (FlgE), and pilus periplasmic chaperone) were shortlisted for the epitope prediction. The predicted epitopes were checked for antigenicity, toxicity, solubility, and binding affinity with the DRB*0101 allele. The selected epitopes were linked with each other through GPGPG linkers and were joined with the cholera toxin B subunit (CTBS) to boost immune responses. The tertiary structure of the vaccine was modeled and blindly docked with MHC-I, MHC-II, and Toll-like receptors 4 (TLR4). Molecular dynamic simulations of 250 nanoseconds affirmed that the designed vaccine showed stable conformation with the receptors. Further, intermolecular binding free energies demonstrated the domination of both the van der Waals and electrostatic energies. Overall, the results of the current study might help experimentalists to develop a novel vaccine against M. morganii.<\/jats:p>","DOI":"10.3390\/ijerph182010961","type":"journal-article","created":{"date-parts":[[2021,10,20]],"date-time":"2021-10-20T03:01:13Z","timestamp":1634698873000},"page":"10961","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":44,"title":["Towards A Novel Multi-Epitopes Chimeric Vaccine for Simulating Strong Immune Responses and Protection against Morganella morganii"],"prefix":"10.3390","volume":"18","author":[{"given":"Asad","family":"Ullah","sequence":"first","affiliation":[{"name":"Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sajjad","family":"Ahmad","sequence":"additional","affiliation":[{"name":"Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8793-2972","authenticated-orcid":false,"given":"Saba","family":"Ismail","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zobia","family":"Afsheen","sequence":"additional","affiliation":[{"name":"Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8375-8532","authenticated-orcid":false,"given":"Muhammad","family":"Khurram","sequence":"additional","affiliation":[{"name":"Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan"},{"name":"Department of Pharmacy, Abasyn University, Peshawar 25000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4832-4250","authenticated-orcid":false,"given":"Muhammad","family":"Tahir ul Qamar","sequence":"additional","affiliation":[{"name":"College of Life Science and Technology, Guangxi University, Nanning 530004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naif","family":"AlSuhaymi","sequence":"additional","affiliation":[{"name":"Department of Emergency Medical Services, Faculty of Health Sciences, AlQunfudah, Umm Al-Qura University, Makkah 21912, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mahdi H.","family":"Alsugoor","sequence":"additional","affiliation":[{"name":"Department of Emergency Medical Services, Faculty of Health Sciences, AlQunfudah, Umm Al-Qura University, Makkah 21912, 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":[[2021,10,19]]},"reference":[{"key":"ref_1","unstructured":"Edwards, M., Hamilton, R., Oliver, N., Fitzgibbon, S., and Samarasekera, R. (2019). Antibiotic Resistance: Modelling the Impact on Mortality and Morbidity. Institute and Faculty of Actuaries."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"36","DOI":"10.4103\/jgid.jgid_110_18","article-title":"Global contributors to antibiotic resistance","volume":"11","author":"Sifri","year":"2019","journal-title":"J. Glob. Infect. Dis."},{"key":"ref_3","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_4","first-page":"277","article-title":"The antibiotic resistance crisis: Part 1: Causes and threats","volume":"40","author":"Ventola","year":"2015","journal-title":"Pharm. Ther."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1722","DOI":"10.3389\/fimmu.2019.01722","article-title":"Vaccine Evolution and Its Application to Fight Modern Threats","volume":"10","author":"Andreano","year":"2019","journal-title":"Front. Immunol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"184","DOI":"10.4161\/hv.4.3.6313","article-title":"Genome-based vaccine development: A short cut for the future","volume":"4","author":"Moriel","year":"2008","journal-title":"Hum. Vaccines"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/j.biologicals.2017.08.004","article-title":"Towards a peptide-based vaccine against Shigella sonnei: A subtractive reverse vaccinology based approach","volume":"50","author":"Baseer","year":"2017","journal-title":"Biology"},{"key":"ref_8","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_9","first-page":"12","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_10","first-page":"1","article-title":"Pan-Genome Analysis of Human Gastric Pathogen H. pylori: Comparative Genomics and Pathogenomics Approaches to Identify Regions Associated with Pathogenicity and Prediction of Potential Core Therapeutic Targets","volume":"2015","author":"Ali","year":"2015","journal-title":"BioMed Res. Int."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1016\/S0264-410X(02)00566-2","article-title":"Two years into reverse vaccinology","volume":"21","author":"Capecchi","year":"2003","journal-title":"Vaccine"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.ijid.2017.01.032","article-title":"Immune response and protective profile elicited by a multi-epitope chimeric protein derived from Leptospira interrogans","volume":"57","author":"Fernandes","year":"2017","journal-title":"Int. J. Infect. Dis."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Naz, K., Naz, A., Ashraf, S.T., Rizwan, M., Ahmad, J., Baumbach, J., and Ali, A. (2019). PanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome. BMC Bioinform., 20.","DOI":"10.1186\/s12859-019-2713-9"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"76","DOI":"10.1177\/2051013615579869","article-title":"Group B Streptococcus vaccine: State of the art","volume":"3","author":"Nuccitelli","year":"2015","journal-title":"Ther. Adv. Vaccines"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1111\/lam.13237","article-title":"Genomic analysis of two drug-resistant clinical Morganella morganii strains isolated from UTI patients in Pretoria, South Africa","volume":"70","author":"Mbelle","year":"2020","journal-title":"Lett. Appl. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"D12","DOI":"10.1093\/nar\/gkw1071","article-title":"Database Resources of the National Center for Biotechnology Information","volume":"45","author":"Coordinators","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"24373","DOI":"10.1038\/srep24373","article-title":"BPGA- an ultra-fast pan-genome analysis pipeline","volume":"6","author":"Chaudhari","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"e20046","DOI":"10.1002\/tpg2.20046","article-title":"Pan-genome: A promising resource for noncoding RNA discovery in plants","volume":"13","author":"Qamar","year":"2020","journal-title":"Plant. Genome"},{"key":"ref_19","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."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.jmgm.2018.04.005","article-title":"Comparative subtractive proteomics based ranking for antibiotic targets against the dirtiest superbug: Acinetobacter baumannii","volume":"82","author":"Ahmad","year":"2018","journal-title":"J. Mol. Graph. Model."},{"key":"ref_21","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":"Qamar","year":"2021","journal-title":"Comput. Biol. Med."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1608","DOI":"10.1093\/bioinformatics\/btq249","article-title":"PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes","volume":"26","author":"Yu","year":"2010","journal-title":"Bioinformatics"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"D687","DOI":"10.1093\/nar\/gky1080","article-title":"VFDB 2019: A comparative pathogenomic platform with an interactive web interface","volume":"47","author":"Liu","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Doytchinova, I.A., and Flower, D.R. (2007). VaxiJen: A server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinform., 8.","DOI":"10.1186\/1471-2105-8-4"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2278","DOI":"10.1007\/s00894-014-2278-5","article-title":"AllerTOP v. 2\u2014A server for in silico prediction of allergens","volume":"20","author":"Dimitrov","year":"2014","journal-title":"J. Mol. Model."},{"key":"ref_26","first-page":"D6","article-title":"Basic local alignment search tool","volume":"43(D1)","author":"Blast","year":"2015","journal-title":"Natl. Libr. Med. Natl. Cent. Biotechnol. Inf."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1007\/s00335-003-2296-6","article-title":"Secreted protein prediction system combining CJ-SPHMM, TMHMM, and PSORT","volume":"14","author":"Chen","year":"2003","journal-title":"Mamm. Genome"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.ejps.2019.02.023","article-title":"Combating tigecycline resistant Acinetobacter baumannii: A leap forward towards multi-epitope based vaccine discovery","volume":"132","author":"Ahmad","year":"2019","journal-title":"Eur. J. Pharm. Sci."},{"key":"ref_29","unstructured":"ProtParam, E. ExPASy-ProtParam Tool 2017."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1016\/j.compbiolchem.2016.04.006","article-title":"Designing an efficient multi-epitope peptide vaccine against Vibrio cholerae via combined immunoinformatics and protein interaction based approaches","volume":"62","author":"Nezafat","year":"2016","journal-title":"Comput. Biol. Chem."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1080\/14760584.2020.1811091","article-title":"Designing an efficient multi-epitope vaccine displaying interactions with diverse HLA molecules for an efficient humoral and cellular immune response to prevent COVID-19 infection","volume":"19","author":"Mahapatra","year":"2020","journal-title":"Expert Rev. Vaccines"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"107477","DOI":"10.1016\/j.jmgm.2019.107477","article-title":"In silico screening of antigenic B-cell derived T-cell epitopes and designing of a multi-epitope peptide vaccine for Acinetobacter nosocomialis","volume":"94","author":"Sajjad","year":"2020","journal-title":"J. Mol. Graph. Model."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"W24","DOI":"10.1093\/nar\/gkx346","article-title":"BepiPred-2.0: Improving sequence-based B-cell epitope prediction using conformational epitopes","volume":"45","author":"Jespersen","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"104382","DOI":"10.1016\/j.meegid.2020.104382","article-title":"Understanding the B and T cell epitopes of spike protein of severe acute respiratory syndrome coronavirus-2: A computational way to predict the immunogens","volume":"84","author":"Vashi","year":"2020","journal-title":"Infect. Genet. Evol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"D405","DOI":"10.1093\/nar\/gku938","article-title":"The immune epitope database (IEDB) 3.0","volume":"43","author":"Vita","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"113612","DOI":"10.1016\/j.molliq.2020.113612","article-title":"Immunoinformatics characterization of SARS-CoV-2 spike glycoprotein for prioritization of epitope based multivalent peptide vaccine","volume":"314","author":"Ismail","year":"2020","journal-title":"J. Mol. Liq."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1016\/j.meegid.2015.03.027","article-title":"Identification of putative vaccine candidates against Helicobacter pylori exploiting exoproteome and secretome: A reverse vaccinology based approach","volume":"32","author":"Naz","year":"2015","journal-title":"Infect. Genet. Evol."},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Gupta, S., Kapoor, P., Chaudhary, K., Gautam, A., Kumar, R., Raghava, G.P.S., and Consortium, O.S.D.D. (2013). Others in silico approach for predicting toxicity of peptides and proteins. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0073957"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1093\/bioinformatics\/btaa1102","article-title":"SoluProt: Prediction of soluble protein expression in Escherichia coli","volume":"37","author":"Hon","year":"2021","journal-title":"Bioinformatics"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"515","DOI":"10.3390\/vaccines2030515","article-title":"Peptide Vaccine: Progress and Challenges","volume":"2","author":"Li","year":"2014","journal-title":"Vaccines"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1038\/cmi.2017.92","article-title":"Multi-epitope vaccines: A promising strategy against tumors and viral infections","volume":"15","author":"Zhang","year":"2018","journal-title":"Cell. Mol. Immunol."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"104970","DOI":"10.1016\/j.micpath.2021.104970","article-title":"Design, expression, and purification of a multi-epitope vaccine against Helicobacter pylori based on Melittin as an adjuvant","volume":"157","author":"Jafari","year":"2021","journal-title":"Microb. Pathog."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"579","DOI":"10.3390\/vaccines3030579","article-title":"Cholera Toxin Subunit B as Adjuvant\u2014An Accelerator in Protective Immunity and a Break in Autoimmunity","volume":"3","author":"Stratmann","year":"2015","journal-title":"Vaccines"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"W72","DOI":"10.1093\/nar\/gki396","article-title":"SCRATCH: A protein structure and structural feature prediction server","volume":"33","author":"Cheng","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1101\/gr.4086505","article-title":"Galaxy: A platform for interactive large-scale genome analysis","volume":"15","author":"Giardine","year":"2005","journal-title":"Genome Res."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"W384","DOI":"10.1093\/nar\/gkt458","article-title":"GalaxyRefine: Protein structure refinement driven by side-chain repacking","volume":"41","author":"Heo","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Craig, D.B., and Dombkowski, A.A. (2013). Disulfide by Design 2.0: A web-based tool for disulfide engineering in proteins. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-346"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"650","DOI":"10.1002\/biot.201000332","article-title":"Codon usage: Nature\u2019s roadmap to expression and folding of proteins","volume":"6","author":"Angov","year":"2011","journal-title":"Biotechnol. J."},{"key":"ref_49","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_50","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_51","doi-asserted-by":"crossref","first-page":"W229","DOI":"10.1093\/nar\/gkn186","article-title":"FireDock: A web server for fast interaction refinement in molecular docking","volume":"36","author":"Mashiach","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"ref_52","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_53","unstructured":"Case, D.A., Belfon, K., Ben-Shalom, I., Brozell, S.R., Cerutti, D., Cheatham, T., Cruzeiro, V.W.D., Darden, T., Duke, R.E., and Giambasu, G. (2020). Amber, University of California."},{"key":"ref_54","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_55","first-page":"U403","article-title":"Antechamber: An accessory software package for molecular mechanical calculations","volume":"222","author":"Wang","year":"2001","journal-title":"J. Am. Chem. Soc."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"3696","DOI":"10.1021\/acs.jctc.5b00255","article-title":"ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB","volume":"11","author":"Maier","year":"2015","journal-title":"J. Chem. Theory Comput."},{"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":"52118","DOI":"10.1103\/PhysRevE.100.052118","article-title":"Zeros of partition functions in the N P T ensemble","volume":"100","author":"Aslyamov","year":"2019","journal-title":"Phys. Rev. E"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"3084","DOI":"10.1021\/ct400341p","article-title":"PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data","volume":"9","author":"Roe","year":"2013","journal-title":"J. Chem. Theory Comput."},{"key":"ref_61","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_62","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.pdf","volume":"51","author":"Hou","year":"2011","journal-title":"J. Chem. Inf. Model."},{"key":"ref_63","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_64","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_65","doi-asserted-by":"crossref","first-page":"147","DOI":"10.1016\/j.genrep.2017.04.008","article-title":"Identification of plausible drug targets by investigating the druggable genome of MDR Staphylococcus epidermidis","volume":"7","author":"Sanober","year":"2017","journal-title":"Gene Rep."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Barh, D., Barve, N., Gupta, K., Chandra, S., Jain, N., Tiwari, S., Leon-Sicairos, N., Canizalez-Roman, A., Santos, A., and Hassan, S.S. (2013). Exoproteome and Secretome Derived Broad Spectrum Novel Drug and Vaccine Candidates in Vibrio cholerae Targeted by Piper betel Derived Compounds. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0052773"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1016\/j.micpath.2017.12.063","article-title":"Subtractive genome analysis for in silico identification and characterization of novel drug targets in Streptococcus pneumonia strain JJA","volume":"115","author":"Wadood","year":"2018","journal-title":"Microb. Pathog."},{"key":"ref_68","doi-asserted-by":"crossref","unstructured":"Ebihara, T. (2020). Dichotomous Regulation of Acquired Immunity by Innate Lymphoid Cells. Cells, 9.","DOI":"10.3390\/cells9051193"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"S33","DOI":"10.1016\/j.jaci.2009.09.017","article-title":"Adaptive immunity","volume":"125","author":"Bonilla","year":"2010","journal-title":"J. Allergy Clin. Immunol."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12936-021-03810-2","article-title":"Humoral and cellular immune response to Plasmodium vivax VIR recombinant and synthetic antigens in individuals naturally exposed to P. vivax in the Republic of Korea","volume":"20","author":"Lee","year":"2021","journal-title":"Malar. J."},{"key":"ref_71","first-page":"2680160","article-title":"Fundamentals and Methods for T- and B-Cell Epitope Prediction","volume":"2017","author":"Reche","year":"2017","journal-title":"J. Immunol. Res."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1016\/j.febslet.2013.11.024","article-title":"Protein disulfide engineering","volume":"588","author":"Dombkowski","year":"2014","journal-title":"FEBS Lett."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1111\/1751-7915.13332","article-title":"Improved protein production and codon optimization analyses in Escherichia coli by bicistronic design","volume":"12","author":"Nieuwkoop","year":"2018","journal-title":"Microb. Biotechnol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"625","DOI":"10.1006\/jmbi.1994.1017","article-title":"Significance of Root-Mean-Square Deviation in Comparing Three-dimensional Structures of Globular Proteins","volume":"235","author":"Maiorov","year":"1994","journal-title":"J. Mol. Biol."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1016\/j.jmgm.2017.07.024","article-title":"Binding mode analysis, dynamic simulation and binding free energy calculations of the MurF ligase from Acinetobacter baumannii","volume":"77","author":"Ahmad","year":"2017","journal-title":"J. Mol. Graph. Model."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1134\/S0026893308040195","article-title":"V Radius of gyration as an indicator of protein structure compactness","volume":"42","author":"Lobanov","year":"2008","journal-title":"Mol. Biol."},{"key":"ref_77","doi-asserted-by":"crossref","unstructured":"Chen, L., Yuan, J., Xu, Y., Zhang, F., and Chen, Z. (2018). Comparison of clinical manifestations and antibiotic resistances among three genospecies of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0191748"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"318","DOI":"10.1016\/S1473-3099(17)30753-3","article-title":"Discovery, research, and development of new antibiotics: The WHO priority list of antibiotic-resistant bacteria and tuberculosis","volume":"18","author":"Tacconelli","year":"2018","journal-title":"Lancet Infect. Dis."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1038\/s41579-020-00506-3","article-title":"The role of vaccines in combatting antimicrobial resistance","volume":"19","author":"Micoli","year":"2021","journal-title":"Nat. Rev. Microbiol. Genet."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1016\/j.meegid.2019.06.006","article-title":"Immunoinformatics and structural vaccinology driven prediction of multi-epitope vaccine against Mayaro virus and validation through in-silico expression","volume":"73","author":"Khan","year":"2019","journal-title":"Infect. Genet. Evol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"104412","DOI":"10.1016\/j.compbiomed.2021.104412","article-title":"Genome-wide screening of vaccine targets prioritization and reverse vaccinology aided design of peptides vaccine to enforce humoral immune response against Campylobacter jejuni","volume":"133","author":"Zeb","year":"2021","journal-title":"Comput. Biol. Med."},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1016\/S0264-410X(00)00554-5","article-title":"Reverse vaccinology, a genome-based approach to vaccine development","volume":"19","author":"Rappuoli","year":"2001","journal-title":"Vaccine"},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/j.sbi.2021.01.002","article-title":"Outer membrane protein evolution","volume":"68","author":"Dhar","year":"2021","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"eabf2403","DOI":"10.1126\/sciadv.abf2403","article-title":"The mycoplasma surface proteins MIB and MIP promote the dissociation of the antibody-antigen interaction","volume":"7","author":"Nottelet","year":"2021","journal-title":"Sci. Adv."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"2121","DOI":"10.1016\/j.xphs.2020.12.012","article-title":"Physicochemical Characterization of Sabin Inactivated Poliovirus Vaccine for Process Development","volume":"110","author":"Torisu","year":"2021","journal-title":"J. Pharm. Sci."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"100718","DOI":"10.1016\/j.imu.2021.100718","article-title":"Immunoinformatic approach for the evaluation of sortase C and E proteins as vaccine targets against Caseous lymphadenitis","volume":"26","author":"Silva","year":"2021","journal-title":"Inform. Med. Unlocked"},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Morris, G.M., and Lim-Wilby, M. (2008). Molecular docking. Molecular Modeling of Proteins, Springer.","DOI":"10.1007\/978-1-59745-177-2_19"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/S0959-440X(02)00308-1","article-title":"Molecular dynamics simulations","volume":"12","author":"Hansson","year":"2002","journal-title":"Curr. Opin. Struct. Biol."},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Hubbard, R.E., and Haider, M.K. (2010). Hydrogen Bonds in Proteins: Role and Strength. eLS, Wiley.","DOI":"10.1002\/9780470015902.a0003011.pub2"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1016\/j.biologicals.2018.07.004","article-title":"Proteome-wide identification of epitope-based vaccine candidates against multi-drug resistant Proteus mirabilis","volume":"55","author":"Ehsan","year":"2018","journal-title":"Biology"},{"key":"ref_91","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2020\/9475058","article-title":"Design of Epitope-Based Peptide Vaccine against Pseudomonas aeruginosa Fructose Bisphosphate Aldolase Protein Using Immunoinformatics","volume":"2020","author":"Elhag","year":"2020","journal-title":"J. Immunol. Res."},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1016\/j.jmgm.2018.01.010","article-title":"Immuno-informatics driven proteome-wide investigation revealed novel peptide-based vaccine targets against emerging multiple drug resistant Providencia stuartii","volume":"80","author":"Asad","year":"2018","journal-title":"J. Mol. Graph. Model."},{"key":"ref_93","doi-asserted-by":"crossref","unstructured":"Dar, H.A., Zaheer, T., Shehroz, M., Ullah, N., Naz, K., Muhammad, S.A., Zhang, T., and Ali, A. (2019). Immunoinformatics-Aided Design and Evaluation of a Potential Multi-Epitope Vaccine against Klebsiella Pneumoniae. Vaccines, 7.","DOI":"10.3390\/vaccines7030088"},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"2857","DOI":"10.1080\/07391102.2020.1756411","article-title":"Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: An in silico study","volume":"39","author":"Enayatkhani","year":"2021","journal-title":"J. Biomol. Struct. Dyn."},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"4850","DOI":"10.1080\/07391102.2019.1692072","article-title":"Proteome-wide screening for designing a multi-epitope vaccine against emerging pathogen Elizabethkingia anophelis using immunoinformatic approaches","volume":"38","author":"Nain","year":"2020","journal-title":"J. Biomol. Struct. Dyn."}],"container-title":["International Journal of Environmental Research and Public Health"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1660-4601\/18\/20\/10961\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:17:39Z","timestamp":1760167059000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1660-4601\/18\/20\/10961"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,10,19]]},"references-count":95,"journal-issue":{"issue":"20","published-online":{"date-parts":[[2021,10]]}},"alternative-id":["ijerph182010961"],"URL":"https:\/\/doi.org\/10.3390\/ijerph182010961","relation":{},"ISSN":["1660-4601"],"issn-type":[{"value":"1660-4601","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,10,19]]}}}