References
- Hallam HJ, Hallam S, Rodriguez SE, et al. Baseline mapping of Lassa fever virology, epidemiology and vaccine research and development. NPJ Vaccines 2018;3:11.
- Rowaiye AB, Oli AN, Onuh OA, et al. Rhamnetin is a better inhibitor of SARS-CoV-2 2'-O-methyltransferase than dolutegravir: a computational prediction. Afr J Infect Dis 2022;16:80-96.
- Ogbu O, Ajuluchukwu E, Uneke CJ. Lassa fever in West African sub-region: an overview. J Vector Borne Dis 2007;44:1-11.
- Merson L, Bourner J, Jalloh S, et al. Clinical characterization of Lassa fever: a systematic review of clinical reports and research to inform clinical trial design. PLoS Negl Trop Dis 2021;15:e0009788.
- Oyeribhor AO. Lived experiences of Lassa fever survivors in Southsouth Nigeria [dissertation]. Minneapolis (MN): Walden University; 2021.
- Fischer RJ, Purushotham JN, van Doremalen N, et al. ChAdOx1-vectored Lassa fever vaccine elicits a robust cellular and humoral immune response and protects guinea pigs against lethal Lassa virus challenge. NPJ Vaccines 2021;6:32.
- Shanmugam A, Rajoria S, George AL, Mittelman A, Suriano R, Tiwari RK. Synthetic Toll like receptor-4 (TLR-4) agonist peptides as a novel class of adjuvants. PLoS One 2012;7:e30839.
- Herrera LR. In silico approach in designing a novel multi-epitope vaccine candidate against non-small cell lung cancer with overexpressed G protein-coupled receptor 56. Asian Pac J Cancer Prev 2020;21:2297-306.
- Dorosti H, Eslami M, Negahdaripour M, et al. Vaccinomics approach for developing multi-epitope peptide pneumococcal vaccine. J Biomol Struct Dyn 2019;37:3524-35.
- Nain Z, Abdulla F, Rahman MM, et al. Proteome-wide screening for designing a multi-epitope vaccine against emerging pathogen Elizabethkingia anophelis using immunoinformatic approaches. J Biomol Struct Dyn 2020;38:4850-67.
- Abdellrazeq GS, Fry LM, Elnaggar MM, et al. Simultaneous cognate epitope recognition by bovine CD4 and CD8 T cells is essential for primary expansion of antigen-specific cytotoxic T-cells following ex vivo stimulation with a candidate Mycobacterium avium subsp. paratuberculosis peptide vaccine. Vaccine 2020;38:2016-25.
- Martin WR, Cheng F. A rational design of a multi-epitope vaccine against SARS-CoV-2 which accounts for the glycan shield of the spike glycoprotein. J Biomol Struct Dyn 2022;40:7099-113.
- Heo L, Park H, Seok C. GalaxyRefine: protein structure refinement driven by side-chain repacking. Nucleic Acids Res 2013;41(Web Server issue):W384-8.
- Schiffrin B, Radford SE, Brockwell DJ, Calabrese AN. PyXlinkViewer: a flexible tool for visualization of protein chemical crosslinking data within the PyMOL molecular graphics system. Protein Sci 2020;29:1851-7.
- Yan Y, Zhang D, Zhou P, Li B, Huang SY. HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy. Nucleic Acids Res 2017;45(W1):W365-73.
- Sharp PM, Li WH. The codon Adaptation Index: a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res 1987;15:1281-95.
- Stokes WA, Glick BS. MICA: desktop software for comprehensive searching of DNA databases. BMC Bioinformatics 2006;7:427.
- Weisblum Y, Schmidt F, Zhang F, et al. Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. Elife 2020;9:e61312.
- Doytchinova IA, Flower DR. VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics 2007;8:4.
- Kumar J, Qureshi R, Sagurthi SR, Qureshi IA. Designing of nucleocapsid protein based novel multi-epitope vaccine against SARS-CoV-2 using immunoinformatics approach. Int J Pept Res Ther 2021;27:941-56.
- Scheiblhofer S, Laimer J, Machado Y, Weiss R, Thalhamer J. Influence of protein fold stability on immunogenicity and its implications for vaccine design. Expert Rev Vaccines 2017;16:479-89.
- Gu H, Liao Y, Zhang J, et al. Rational design and evaluation of an artificial Escherichia coli K1 protein vaccine candidate based on the structure of OmpA. Front Cell Infect Microbiol 2018;8:172.
- Haimov B, Srebnik S. A closer look into the α-helix basin. Sci Rep 2016;6:38341.
- Aldakheel FM, Abrar A, Munir S, et al. Proteome-wide mapping and reverse vaccinology approaches to design a multi-epitope vaccine against Clostridium perfringens. Vaccines (Basel) 2021;9:1079.
- Bonam SR, Partidos CD, Halmuthur SK, Muller S. An overview of novel adjuvants designed for improving vaccine efficacy. Trends Pharmacol Sci 2017;38:771-93.
- Greenbaum JA, Andersen PH, Blythe M, et al. Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J Mol Recognit 2007;20:75-82.
- Erkes DA, Selvan SR. Hapten-induced contact hypersensitivity, autoimmune reactions, and tumor regression: plausibility of mediating antitumor immunity. J Immunol Res 2014;2014:175265.
- Islinger M, Wildgruber R, Volkl A. Preparative free-flow electrophoresis, a versatile technology complementing gradient centrifugation in the isolation of highly purified cell organelles. Electrophoresis 2018;39:2288-99.
- Oladipo EK, Ajayi AF, Ariyo OE, et al. Exploration of surface glycoprotein to design multi-epitope vaccine for the prevention of COVID-19. Inform Med Unlocked 2020;21:100438.
- Habibi N, Mohd Hashim SZ, Norouzi A, Samian MR. A review of machine learning methods to predict the solubility of overexpressed recombinant proteins in Escherichia coli. BMC Bioinformatics 2014;15:134.
- Williams CJ, Headd JJ, Moriarty NW, et al. MolProbity: more and better reference data for improved all-atom structure validation. Protein Sci 2018;27:293-315.
- Navone L, Vogl T, Luangthongkam P, et al. Disulfide bond engineering of AppA phytase for increased thermostability requires co-expression of protein disulfide isomerase in Pichia pastoris. Biotechnol Biofuels 2021;14:80.
- Smith DK, Radivojac P, Obradovic Z, Dunker AK, Zhu G. Improved amino acid flexibility parameters. Protein Sci 2003;12:1060-72.
- Lopez-Blanco JR, Aliaga JI, Quintana-Orti ES, Chacon P. iMODS: internal coordinates normal mode analysis server. Nucleic Acids Res 2014;42(Web Server issue):W271-6.
- Xing Y, Gong R, Xu Y, Liu K, Zhou M. Codon usage bias affects α-amylase mRNA level by altering RNA stability and cytosine methylation patterns in Escherichia coli. Can J Microbiol 2020;66:521-8.
- Lee S, Weon S, Lee S, Kang C. Relative codon adaptation index, a sensitive measure of codon usage bias. Evol Bioinform Online 2010;6:47-55.
- Newman ZR, Young JM, Ingolia NT, Barton GM. Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9. Proc Natl Acad Sci U S A 2016;113:E1362-71.
- Grote A, Hiller K, Scheer M, et al. JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res 2005;33(Web Server issue):W526-31.
- Biocompare. Bench Tips: Primers, by design: tips for optimal DNA primer design [Internet]. San Francisco (CA): Biocompare; 2013 [cited 2021 Mar 8]. Available from: https://www.biocompare.com/Bench-Tips/133581-Primers-by-Design-Tips-for-Optimal-DNA-Primer-Design/.
- Kayama K, Kanno M, Chisaki N, et al. Prediction of PCR amplification from primer and template sequences using recurrent neural network. Sci Rep 2021;11:7493.