{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T06:23:58Z","timestamp":1788157438780,"version":"build-2803163510"},"reference-count":86,"publisher":"MDPI AG","issue":"10","license":[{"start":{"date-parts":[[2021,9,26]],"date-time":"2021-09-26T00:00:00Z","timestamp":1632614400000},"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>C. perfringens is a highly versatile bacteria of livestock and humans, causing enteritis (a common food-borne illness in humans), enterotoxaemia (in which toxins are formed in the intestine which damage and destroy organs, i.e., the brain), and gangrene (wound infection). There is no particular cure for the toxins of C. perfringens. Supportive care (medical control of pain, intravenous fluids) is the standard treatment. Therefore, a multiple-epitope vaccine (MEV) should be designed to battle against C. perfringens infection. Furthermore, the main objective of this in silico investigation is to design an MEV that targets C. perfringens. For this purpose, we selected the top three proteins that were highly antigenic using immuno-informatics approaches, including molecular docking. B-cells, IFN-gamma, and T cells for target proteins were predicted and the most conserved epitopes were selected for further investigation. For the development of the final MEV, epitopes of LBL5, CTL17, and HTL13 were linked to GPGPG, AAY, and KK linkers. The vaccine N-end was joined to an adjuvant through an EAAK linker to improve immunogenicity. After the attachment of linkers and adjuvants, the final construct was 415 amino acids. B-cell and IFN-gamma epitopes demonstrate that the model structure is enhanced for humoral and cellular immune responses. To validate the immunogenicity and safety of the final construct, various physicochemical properties, and other properties such as antigenicity and non-allergens, were evaluated. Furthermore, molecular docking was carried out for verification of vaccine compatibility with the receptor, evaluated in silico. Also, in silico cloning was employed for the verification of the proper expression and credibility of the construct.<\/jats:p>","DOI":"10.3390\/vaccines9101079","type":"journal-article","created":{"date-parts":[[2021,9,27]],"date-time":"2021-09-27T23:08:31Z","timestamp":1632784111000},"page":"1079","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Proteome-Wide Mapping and Reverse Vaccinology Approaches to Design a Multi-Epitope Vaccine against Clostridium perfringens"],"prefix":"10.3390","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8047-8650","authenticated-orcid":false,"given":"Fahad M.","family":"Aldakheel","sequence":"first","affiliation":[{"name":"Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11564, Saudi Arabia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amna","family":"Abrar","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samman","family":"Munir","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sehar","family":"Aslam","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan"}],"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"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3196-2857","authenticated-orcid":false,"given":"Mohsin","family":"Khurshid","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Government College University, Faisalabad 38000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5495-805X","authenticated-orcid":false,"given":"Usman Ali","family":"Ashfaq","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Biotechnology, Government College University, Faisalabad 38000, Pakistan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,9,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Forti, K., Ferroni, L., Pellegrini, M., Cruciani, D., De Giuseppe, A., Crotti, S., Papa, P., Maresca, C., Severi, G., and Marenzoni, M.L. (2020). Molecular characterization of clostridium perfringens strains isolated in Italy. Toxins, 12.","DOI":"10.3390\/toxins12100650"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1093\/cid\/ciw016","article-title":"A Necrotizing enterocolitis-associated gut microbiota is present in the meconium: Results of a prospective study","volume":"62","author":"Heida","year":"2016","journal-title":"Clin. Infect. Dis."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"6756","DOI":"10.1038\/s41598-021-86148-8","article-title":"Comparative in silico genome analysis of Clostridium perfringens unravels stable phylogroups with different genome characteristics and pathogenic potential","volume":"11","author":"Thomas","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1586\/erv.11.54","article-title":"Strategies for and advances in the development of Staphylococcus aureusprophylactic vaccines","volume":"10","author":"Broughan","year":"2011","journal-title":"Expert Rev. Vaccines"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2921","DOI":"10.1016\/j.vaccine.2011.11.006","article-title":"Is there a future for a Staphylococcus aureus vaccine?","volume":"30","author":"Proctor","year":"2012","journal-title":"Vaccine"},{"key":"ref_6","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_7","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_8","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1016\/j.coviro.2015.03.001","article-title":"Lessons from reverse vaccinology for viral vaccine design","volume":"11","author":"Bruno","year":"2015","journal-title":"Curr. Opin. Virol."},{"key":"ref_9","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_10","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_11","doi-asserted-by":"crossref","first-page":"2089","DOI":"10.1007\/s10989-019-10003-8","article-title":"Exploring lassa virus proteome to design a multi-epitope vaccine through immunoinformatics and immune simulation analyses","volume":"26","author":"Nain","year":"2020","journal-title":"Int. J. Pept. Res. Ther."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"1125","DOI":"10.1038\/s41598-018-19456-1","article-title":"Novel Immunoinformatics approaches to design multi-epitope subunit vaccine for malaria by investigating anopheles salivary protein","volume":"8","author":"Pandey","year":"2018","journal-title":"Sci. Rep."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"4409","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_14","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1080\/20477724.2018.1446773","article-title":"Current progress of immunoinformatics approach harnessed for cellular- and antibody-dependent vaccine design","volume":"112","author":"Kazi","year":"2018","journal-title":"Pathog. Glob. Health"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1007\/978-1-4939-3167-5_2","article-title":"UniProtKB\/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase: How to use the entry view","volume":"1374","author":"Boutet","year":"2016","journal-title":"Methods Mol. Biol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"9044","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_17","doi-asserted-by":"crossref","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: Accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1236","DOI":"10.3389\/fmicb.2019.01236","article-title":"Geptop 2.0: An updated, more precise, and faster geptop server for identification of prokaryotic essential genes","volume":"10","author":"Wen","year":"2019","journal-title":"Front. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1016\/j.resmic.2008.03.005","article-title":"Unifying classical and molecular taxonomic classification: Analysis of the Podoviridae using BLASTP-based tools","volume":"159","author":"Lavigne","year":"2008","journal-title":"Res. Microbiol."},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Azhagesan, K., Ravindran, B., and Raman, K. (2018). Network-based features enable prediction of essential genes across diverse organisms. PLoS ONE, 13.","DOI":"10.1371\/journal.pone.0208722"},{"key":"ref_21","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_22","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_23","doi-asserted-by":"crossref","first-page":"617","DOI":"10.1093\/bioinformatics\/bti057","article-title":"PSORTb v2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis","volume":"21","author":"Gardy","year":"2004","journal-title":"Bioinformatics"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Yu, C.-S., Cheng, C.-W., Su, W.-C., Chang, S.-C., Huang, S.-W., Hwang, J.-K., and Lu, C.-H. (2014). CELLO2GO: A web server for protein subCELlular LOcalization prediction with functional gene ontology annotation. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0099368"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1038\/nbt1215","article-title":"A consensus epitope prediction approach identifies the breadth of murine T(CD8+)-cell responses to vaccinia virus","volume":"24","author":"Moutaftsi","year":"2006","journal-title":"Nat. Biotechnol."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Calis, J.J.A., Maybeno, M., Greenbaum, J.A., Weiskopf, D., De Silva, A.D., Sette, A., Ke\u015fmir, C., and Peters, B. (2013). Properties of MHC class I presented peptides that enhance immunogenicity. PLoS Comput. Biol., 9.","DOI":"10.1371\/journal.pcbi.1003266"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"2278","DOI":"10.1007\/s00894-014-2278-5","article-title":"AllerTOP v2\u2014A server for in silico prediction of allergens","volume":"20","author":"Dimitrov","year":"2014","journal-title":"J. Mol. Model."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Gupta, S., Kapoor, P., Chaudhary, K., Gautam, A., Kumar, R., Raghava, G.P.S., and Open Source Drug Discovery Consortium (2013). In silico approach for predicting toxicity of peptides and proteins. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0073957"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Nielsen, M., Lundegaard, C., and Lund, O. (2007). Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinform., 8.","DOI":"10.1186\/1471-2105-8-238"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"1122","DOI":"10.1038\/ni.1647","article-title":"Distinct functions for the transcription factors GATA-3 and ThPOK during intrathymic differentiation of CD4+ T cells","volume":"9","author":"Wang","year":"2008","journal-title":"Nat. Immunol."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Wang, Y., Wang, J.J., Wang, W.Y., Mei, Z.G., Shang, S.L., Chen, L.-Q., and Liu, Z.-K. (2010). A mixed-space approach to first-principles calculations of phonon frequencies for polar materials. J. Phys. Condens. Matter, 22.","DOI":"10.1088\/0953-8984\/22\/20\/202201"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"30","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_33","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1038\/nri3801","article-title":"The early history of B cells","volume":"15","author":"Cooper","year":"2015","journal-title":"Nat. Rev. Immunol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1002\/prot.21078","article-title":"Prediction of continuous B-cell epitopes in an antigen using recurrent neural network","volume":"65","author":"Saha","year":"2006","journal-title":"Proteins Struct. Funct. Bioinform."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"1303","DOI":"10.1007\/s10989-019-09933-0","article-title":"Identification of potent vaccine candidates against campylobacter jejuni using immunoinformatics approach","volume":"26","author":"Gupta","year":"2019","journal-title":"Int. J. Pept. Res. Ther."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1684","DOI":"10.1016\/S0140-6736(18)31891-9","article-title":"Global, regional, and national age-sex-specific mortality and life expectancy, 1950\u20132017: A systematic analysis for the Global Burden of Disease Study 2017","volume":"392","author":"Dicker","year":"2018","journal-title":"Lancet"},{"key":"ref_37","doi-asserted-by":"crossref","unstructured":"Bui, H.-H., Sidney, J., Dinh, K., Southwood, S., Newman, M.J., and Sette, A. (2006). Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinform., 7.","DOI":"10.1186\/1471-2105-7-153"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Samad, A., Ahammad, F., Nain, Z., Alam, R., Imon, R.R., Hasan, M., and Rahman, M.S. (2020). Designing a multi-epitope vaccine against SARS-CoV-2: An immunoinformatics approach. J. Biomol. Struct. Dyn., 1\u201317.","DOI":"10.1080\/07391102.2020.1792347"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1016\/j.jtbi.2014.01.018","article-title":"A novel multi-epitope peptide vaccine against cancer: An in silico approach","volume":"349","author":"Nezafat","year":"2014","journal-title":"J. Theor. Biol."},{"key":"ref_40","doi-asserted-by":"crossref","unstructured":"Mahram, A., and Herbordt, M.C. (2010, January 2\u20134). Fast and accurate NCBI BLASTP: Acceleration with multiphase FPGA-based prefiltering. Proceedings of the 24th ACM International Conference on Supercomputing, Tsukuba, Japan.","DOI":"10.1145\/1810085.1810099"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1002\/elps.11501401163","article-title":"The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences","volume":"14","author":"Bjellqvist","year":"1993","journal-title":"Electrophoresis"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1093\/bioinformatics\/16.4.404","article-title":"The PSIPRED protein structure prediction server","volume":"16","author":"McGuffin","year":"2000","journal-title":"Bioinformatics"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1149","DOI":"10.1002\/prot.25792","article-title":"Deep-learning contact-map guided protein structure prediction in CASP13","volume":"87","author":"Zheng","year":"2019","journal-title":"Proteins Struct. Funct. Bioinform."},{"key":"ref_44","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_45","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1002\/prot.10286","article-title":"Structure validation by C\u03b1 geometry: \u03d5, \u03c8 and C\u03b2 deviation","volume":"50","author":"Lovell","year":"2003","journal-title":"Proteins Struct. Funct. Bioinform."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Ponomarenko, J.V., Bui, H.-H., Li, W., Fusseder, N., Bourne, P.E., Sette, A., and Peters, B. (2008). ElliPro: A new structure-based tool for the prediction of antibody epitopes. BMC Bioinform., 9.","DOI":"10.1186\/1471-2105-9-514"},{"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":"816","DOI":"10.1038\/sj.cdd.4401850","article-title":"TLR signaling","volume":"13","author":"Kawai","year":"2006","journal-title":"Cell Death Differ."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1016\/j.drudis.2018.01.015","article-title":"Recent progress in the discovery of myeloid differentiation 2 (MD2) modulators for inflammatory diseases","volume":"23","author":"Chen","year":"2018","journal-title":"Drug Discov. Today"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1007\/s12035-013-8425-7","article-title":"Role of the toll like receptor (TLR) radical cycle in chronic inflammation: Possible treatments targeting the TLR4 pathway","volume":"48","author":"Lucas","year":"2013","journal-title":"Mol. Neurobiol."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"720","DOI":"10.1016\/j.jmb.2015.09.014","article-title":"The HADDOCK2.2 web server: User-friendly integrative modeling of biomolecular complexes","volume":"428","author":"Rodrigues","year":"2016","journal-title":"J. Mol. Biol."},{"key":"ref_52","doi-asserted-by":"crossref","unstructured":"Alexander, N., Woetzel, N., and Meiler, J. (2011, January 3\u20135). Bcl:Cluster: A method for clustering biological molecules coupled with visualization in the Pymol Molecular Graphics System. Proceedings of the 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Orlando, FL, USA.","DOI":"10.1109\/ICCABS.2011.5729867"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"D355","DOI":"10.1093\/nar\/gkn860","article-title":"PDBsum new things","volume":"37","author":"Laskowski","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1002\/(SICI)1096-987X(19970130)18:2<169::AID-JCC3>3.0.CO;2-T","article-title":"A comparison of techniques for calculating protein essential dynamics","volume":"18","author":"Findlay","year":"1997","journal-title":"J. Comput. Chem."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"W271","DOI":"10.1093\/nar\/gku339","article-title":"iMODS: Internal coordinates normal mode analysis server","volume":"42","author":"Aliaga","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"ref_56","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_57","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_58","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1093\/nar\/15.3.1281","article-title":"The codon adaptation index-a measure of directional synonymous codon usage bias, and its potential applications","volume":"15","author":"Sharp","year":"1987","journal-title":"Nucleic Acids Res."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"17118","DOI":"10.1038\/s41598-021-94488-8","article-title":"In-silico design of envelope based multi-epitope vaccine candidate against Kyasanur forest disease virus","volume":"11","author":"Arumugam","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"104795","DOI":"10.1016\/j.meegid.2021.104795","article-title":"Rational design of multimeric based subunit vaccine against Mycoplasma pneumonia: Subtractive proteomics with immunoinformatics framework","volume":"91","author":"Mahmood","year":"2021","journal-title":"Infect. Genet. Evol."},{"key":"ref_61","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_62","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1093\/protein\/14.8.529","article-title":"Design of the linkers which effectively separate domains of a bifunctional fusion protein","volume":"14","author":"Arai","year":"2001","journal-title":"Protein Eng. Des. Sel."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1016\/j.coi.2008.03.003","article-title":"Cytokine-producing B lymphocytes\u2014Key regulators of immunity","volume":"20","author":"Lund","year":"2008","journal-title":"Curr. Opin. Immunol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1002\/prot.20151","article-title":"Predictions of protein flexibility: First-order measures","volume":"56","author":"Kovacs","year":"2004","journal-title":"Proteins Struct. Funct. Bioinform."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"361","DOI":"10.2217\/fmb.13.168","article-title":"Towards an understanding of the role of Clostridium perfringens toxins in human and animal disease","volume":"9","author":"Uzal","year":"2014","journal-title":"Future Microbiol."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"e00500","DOI":"10.1128\/mSphere.00500-20","article-title":"The Agr-like quorum-sensing system is important for clostridium perfringens type A strain ATCC 3624 to cause gas gangrene in a mouse model","volume":"5","author":"Navarro","year":"2020","journal-title":"mSphere"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1128\/JVI.01505-07","article-title":"Rational design of a multiepitope vaccine encoding T-lymphocyte epitopes for treatment of chronic hepatitis B virus infections","volume":"82","author":"Depla","year":"2008","journal-title":"J. Virol."},{"key":"ref_68","first-page":"3","article-title":"The impact of bioinformatics on vaccine design and development","volume":"2","author":"Arturo","year":"2017","journal-title":"Vaccines"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1111\/j.1469-0691.2012.03939.x","article-title":"Developing vaccines in the era of genomics: A decade of reverse vaccinology","volume":"18","author":"Seib","year":"2012","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/B978-0-12-396548-6.00007-X","article-title":"TLR ligand\u2013peptide conjugate vaccines: Toward clinical application","volume":"114","author":"Zom","year":"2012","journal-title":"Adv. Immunol."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"1342","DOI":"10.7150\/ijms.21875","article-title":"Peptides as therapeutic agents for dengue virus","volume":"14","author":"Chew","year":"2017","journal-title":"Int. J. Med Sci."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"37313","DOI":"10.1038\/srep37313","article-title":"Towards peptide vaccines against Zika virus: Immunoinformatics combined with molecular dynamics simulations to predict antigenic epitopes of Zika viral proteins","volume":"6","author":"Mirza","year":"2016","journal-title":"Sci. Rep."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1007\/s11033-018-4505-0","article-title":"Designing of an epitope-based peptide vaccine against walking pneumonia: An immunoinformatics approach","volume":"46","author":"Unni","year":"2019","journal-title":"Mol. Biol. Rep."},{"key":"ref_74","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_75","doi-asserted-by":"crossref","first-page":"121s","DOI":"10.1038\/jid.1984.33","article-title":"The role of antibody and complement in the control of viral infections","volume":"83","author":"Cooper","year":"1984","journal-title":"J. Investig. Dermatol."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1007\/BF02788751","article-title":"The optimization of helper T lymphocyte (HTL) function in vaccine development","volume":"18","author":"Alexander","year":"1998","journal-title":"Immunol. Res."},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1016\/j.compbiomed.2016.06.015","article-title":"Effect of linker length and residues on the structure and stability of a fusion protein with malaria vaccine application","volume":"76","author":"Shamriz","year":"2016","journal-title":"Comput. Biol. Med."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1016\/j.tips.2017.06.002","article-title":"An overview of novel adjuvants designed for improving vaccine efficacy","volume":"38","author":"Bonam","year":"2017","journal-title":"Trends Pharmacol. Sci."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"51","DOI":"10.4110\/in.2015.15.2.51","article-title":"Recent advances of vaccine adjuvants for infectious diseases","volume":"15","author":"Lee","year":"2015","journal-title":"Immune Netw."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"8285","DOI":"10.1038\/s41598-017-08842-w","article-title":"Exploring Leishmania secretory proteins to design B and T cell multi-epitope subunit vaccine using immunoinformatics approach","volume":"7","author":"Khatoon","year":"2017","journal-title":"Sci. Rep."},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Qamar, M.T.U., Rehman, A., Tusleem, K., Ashfaq, U.A., Qasim, M., Zhu, X., Fatima, I., Shahid, F., and Chen, L.-L. (2020). Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics and in silico approaches. PLoS ONE, 15.","DOI":"10.1371\/journal.pone.0244176"},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Qamar, M.T.U., Shokat, Z., Muneer, I., Ashfaq, U.A., Javed, H., Anwar, F., Bari, A., Zahid, B., and Saari, N. (2020). Multiepitope-based subunit vaccine design and evaluation against respiratory syncytial virus using reverse vaccinology approach. Vaccines, 8.","DOI":"10.3390\/vaccines8020288"},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Ismail, S., Ahmad, S., and Azam, S.S. (2020). Immuno-informatics characterization SARS-CoV-2 spike glycoprotein for prioritization of epitope based multivalent peptide vaccine. bioRxiv.","DOI":"10.1101\/2020.04.05.026005"},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/j.jmgm.2018.07.010","article-title":"Investigating the molecular mechanism of staphylococcal DNA gyrase inhibitors: A combined ligand-based and structure-based resources pipeline","volume":"85","author":"Durdagi","year":"2018","journal-title":"J. Mol. Graph. Model."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1007\/s00726-013-1526-9","article-title":"Peptides for immunological purposes: Design, strategies and applications","volume":"45","author":"Gori","year":"2013","journal-title":"Amino Acids"},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"1102","DOI":"10.1016\/j.biotechadv.2011.09.013","article-title":"Bacterial expression systems for recombinant protein production: E. coli and beyond","volume":"30","author":"Chen","year":"2012","journal-title":"Biotechnol. Adv."}],"container-title":["Vaccines"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-393X\/9\/10\/1079\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T07:05:08Z","timestamp":1760166308000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-393X\/9\/10\/1079"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,9,26]]},"references-count":86,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2021,10]]}},"alternative-id":["vaccines9101079"],"URL":"https:\/\/doi.org\/10.3390\/vaccines9101079","relation":{},"ISSN":["2076-393X"],"issn-type":[{"value":"2076-393X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,9,26]]}}}