Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, Lindahl E. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX. 2015;1–2:19–25. https://doi.org/10.1016/j.softx.2015.06.001.

Article  Google Scholar 

Ahmad M, Hirz M, Pichler H, Schwab H. Protein expression in Pichia pastoris: recent achievements and perspectives for heterologous protein production. Appl Microbiol Biotechnol. 2014;98(12):5301–17. https://doi.org/10.1007/s00253-014-5732-5.

Article  PubMed  PubMed Central  Google Scholar 

Ahmed S, Rahman MN, Hasan M, Hasan MA, Mia MMJEP. Immunogenic multi-epitope-based vaccine development to combat cyclosporiasis of immunocompromised patients applying computational biology method. Exp Parasitol. 2023;248:108497. https://doi.org/10.1016/j.exppara.2023.108497

Article  PubMed  Google Scholar 

Alizadeh M, Amini-Khoei H, Tahmasebian S, Ghatrehsamani M, Ghatreh Samani K, Edalatpanah Y, Rostampur S, Salehi M, Ghasemi-Dehnoo M, Azadegan-Dehkordi F, Sanami S, Bagheri N. Designing a novel multi-epitope vaccine against Ebola virus using reverse vaccinology approach. Sci Rep. 2022;12(1): 7757. https://doi.org/10.1038/s41598-022-11851-z.

Article  PubMed  PubMed Central  Google Scholar 

Astuti I, Ysrafil. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2): an overview of viral structure and host response. Diabetes Metab Syndr Clin Res Rev. 2020;14(4):407–412. https://doi.org/10.1016/j.dsx.2020.04.020

Bale JF. Emerging viral infections. Semin Pediatr Neurol. 2012;19(3):152–7. https://doi.org/10.1016/j.spen.2012.02.001.

Article  PubMed  PubMed Central  Google Scholar 

Bartsch SM, O’Shea KJ, John DC, Strych U, Bottazzi ME, Martinez MF, Ciciriello A, Chin KL, Weatherwax C, Velmurugan K, Heneghan J, Scannell SA, Hotez PJ, Lee BY. The potential epidemiologic, clinical, and economic value of a universal coronavirus vaccine: a modelling study. eClinicalMedicine. 2024. https://doi.org/10.1016/j.eclinm.2023.102369.

Article  PubMed  PubMed Central  Google Scholar 

Bui H-H, Sidney J, Dinh K, Southwood S, Newman MJ, Sette A. Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinform. 2006;7(1):153. https://doi.org/10.1186/1471-2105-7-153.

Article  Google Scholar 

Chen M, Hu Z, Shi J, Xie Z. Human β-defensins and their synthetic analogs: natural defenders and prospective new drugs of oral health. Life Sci. 2024;346: 122591.

PubMed  Google Scholar 

Chen Z, Bancej C, Lee L, Champredon DJSR. Antigenic drift and epidemiological severity of seasonal influenza in Canada. Sci Rep. 2022;12(1):15625. https://doi.org/10.1038/s41598-022-19996-7

Article  PubMed  PubMed Central  Google Scholar 

Craven RB, Barnes AM. Plague and tularemia. Infect Dis Clin N Am. 1991;5(1):165–75.

Google Scholar 

de Marco A. Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli. Microb Cell Fact. 2009;8(1):26. https://doi.org/10.1186/1475-2859-8-26.

Article  PubMed  PubMed Central  Google Scholar 

Del Rio C, Malani P. Mpox outbreak update—reply. JAMA. 2023;329(5):428–428. https://doi.org/10.1001/jama.2022.21633

PubMed  Google Scholar 

Dhople V, Krukemeyer A, Ramamoorthy A. The human beta-defensin-3, an antibacterial peptide with multiple biological functions. Biochim Biophys Acta (BBA) Biomembr. 2006;1758(9):1499–512. https://doi.org/10.1016/j.bbamem.2006.07.007.

Article  Google Scholar 

Di Lello FA, Martínez AP, Flichman DM. Insights into induction of the immune response by the hepatitis B vaccine. World J Gastroenterol. 2022;28(31):4249.

PubMed  PubMed Central  Google Scholar 

Dimitrov I, Bangov I, Flower DR, Doytchinova I. AllerTOP v. 2—a server for in silico prediction of allergens. J Mol Model. 2014;20:1–6.

Google Scholar 

Dombkowski AA, Sultana KZ, Craig DB. Protein disulfide engineering. FEBS Lett. 2014;588(2):206–12. https://doi.org/10.1016/j.febslet.2013.11.024.

Article  PubMed  Google Scholar 

Doytchinova IA, Flower DR. Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties. Vaccine. 2007;25(5):856–66.

PubMed  Google Scholar 

Fatima K, Naqvi F, Younas H. A review: molecular chaperone-mediated folding, unfolding and disaggregation of expressed recombinant proteins. Cell Biochem Biophys. 2021;79(2):153–74. https://doi.org/10.1007/s12013-021-00970-5.

Article  PubMed  Google Scholar 

García LF. Immune response, inflammation, and the clinical spectrum of COVID-19. Front Immunol. 2020;11: 1441.

PubMed  PubMed Central  Google Scholar 

Gasteiger E, Hoogland C, Gattiker A, Duvaud SE, Wilkins MR, Appel RD, Bairoch A. Protein identification and analysis tools on the ExPASy server. In: Walker, J.M. (eds) The Proteomics Protocols Handbook. Springer Protocols Handbooks:Humana Press;2005. https://doi.org/10.1385/1-59259-890-0:571

Chapter  Google Scholar 

Geourjon C, Deléage G. SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Bioinformatics. 1995;11(6):681–4. https://doi.org/10.1093/bioinformatics/11.6.681.

Article  Google Scholar 

Ghattas M, Dwivedi G, Lavertu M, Alameh M-G. Vaccine technologies and platforms for infectious diseases: current progress, challenges, and opportunities. Vaccines. 2021;9(12):1490.

PubMed  PubMed Central  Google Scholar 

Gotch F, Hardy G. The immune system: our best antiretroviral. Curr Opin Infect Dis. 2000;13(1):13–7.

PubMed  Google Scholar 

Grote A, Hiller K, Scheer M, Münch R, Nörtemann B, Hempel DC, Jahn D. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res. 2005;33(suppl_2):W526–31. https://doi.org/10.1093/nar/gki376.

Article  PubMed  PubMed Central  Google Scholar 

Gupta S, Kapoor P, Chaudhary K, Gautam A, Kumar R, Open Source Drug Discovery Consortium, Raghava GP. In silico approach for predicting toxicity of peptides and proteins. PLOS One. 2013;8(9):73957. https://doi.org/10.1371/journal.pone.0073957.

Article  Google Scholar 

Guryanova SV, Ovchinnikova TV. Immunomodulatory and allergenic properties of antimicrobial peptides. Int J Mol Sci. 2022. https://doi.org/10.3390/ijms23052499.

Article  PubMed  PubMed Central  Google Scholar 

Gustafsson C, Govindarajan S, Minshull J. Codon bias and heterologous protein expression. Trends Biotechnol. 2004;22(7):346–53. https://doi.org/10.1016/j.tibtech.2004.04.006.

Article  PubMed  Google Scholar 

Hakami MA. An immunoinformatics and structural vaccinology approach to design a novel and potent multi-epitope base vaccine targeting Zika virus. BMC Chem. 2024;18(1):31. https://doi.org/10.1186/s13065-024-01132-3.

Article  PubMed  PubMed Central  Google Scholar 

Hancková M, Betáková TJV. Pandemics of the 21st century: the risk factor for obese people. Viruses. 2021;14(1): 25.

PubMed  PubMed Central  Google Scholar 

Hasan M, Ahmed S, Imranuzzaman M, Bari R, Roy S, Hasan MM, Mia MM. Designing and development of efficient multi-epitope-based peptide vaccine candidate against emerging avian rotavirus strains: a vaccinomic approach. J Genet Eng Biotechnol. 2024;22(3): 100398.

PubMed  PubMed Central  Google Scholar 

Heo L, Park H, Seok C. Galaxyrefine: protein structure refinement driven by side-chain repacking. Nucleic Acids Res. 2013;41(W1):W384–8. https://doi.org/10.1093/nar/gkt458.

Article  PubMed  PubMed Central  Google Scholar 

Hossain MS, Hossan MI, Mizan S, Moin AT, Yasmin F, Akash A-S, Powshi SN, Hasan AKR, Chowdhury AS. Immunoinformatics approach to designing a multi-epitope vaccine against Saint Louis encephalitis virus. Inf Med Unlocked. 2021;22: 100500. https://doi.org/10.1016/j.imu.2020.100500.

Article  Google Scholar 

Hosseini A, Hashemi V, Shomali N, Asghari F, Gharibi T, Akbari M, Gholizadeh S, Jafari A. Innate and adaptive immune responses against coronavirus. Biomed Pharmacother. 2020;132: 110859.

PubMed  PubMed Central  Google Scholar 

Huffman A, Ong E, Hur J, D’Mello A, Tettelin H, He Y. COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning. Brief Bioinform. 2022;23(4): bbac190.

PubMed  PubMed Central  Google Scholar 

Jackson Lisa A, Anderson Evan J, Rouphael Nadine G, Roberts Paul C, Makhene M, Coler Rhea N, Beigel John H. An mRNA vaccine against SARS-CoV-2—preliminary report. New Engl J Med. 2020;383(20):1920–31.