Design peptide and multi-epitope protein vaccine candidates against monkeypox virus using reverse vaccinology approach: an in-silico study

References

• Abraham, M., Van Der Spoel, D., Lindahl, E., & Hess, B. (2014). The GROMACS Development Team. GROMACS User Manual Version 5.0.2.
   Google Scholar
• Alais, S., Mahieux, R., & Dutartre, H. (2015). Viral source-independent high susceptibility of dendritic cells to human T-cell leukemia virus type 1 infection compared to that of T lymphocytes. Journal of Virology, 89(20), 10580–10590. https://doi.org/10.1128/JVI.01799-15
   PubMed Web of Science ®Google Scholar
• Alakunle, E. F., & Okeke, M. I. (2022). Monkeypox virus: A neglected zoonotic pathogen spreads globally. Nature Reviews Microbiology, 20(9), 507–508. https://doi.org/10.1038/s41579-022-00776-z
   PubMed Web of Science ®Google Scholar
• Almehmadi, M., Allahyani, M., Alsaiari, A. A., Alshammari, M. K., Alharbi, A. S., Hussain, K. H., Alsubaihi, L. I., Kamal, M., Alotaibi, S. S., Alotaibi, A. N., Aldhafeeri, A. A., & Imran, M. (2022). A glance at the development and patent literature of tecovirimat: The first-in-class therapy for emerging monkeypox outbreak. Viruses, 14(9), 1870. https://doi.org/10.3390/v14091870
   PubMed Web of Science ®Google Scholar
• Beaufays, J., Lins, L., Thomas, A., & Brasseur, R. (2012). In silico predictions of 3D structures of linear and cyclic peptides with natural and non‐proteinogenic residues. Journal of Peptide Science, 18(1), 17–24. https://doi.org/10.1002/psc.1410
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Iype, L., Schneider, B., & Zardecki, C. (2003). The nucleic acid database. Methods of Biochemical Analysis, 44, 199–216.
   PubMedGoogle Scholar
• Bharti, D. R., Hemrom, A. J., & Lynn, A. M. (2019). GCAC: Galaxy workflow system for predictive model building for virtual screening. BMC Bioinformatics, 19(S13), 199–206. https://doi.org/10.1186/s12859-018-2492-8
   PubMedGoogle Scholar
• Brown, K., & Leggat, P. A. (2016). Human monkeypox: Current state of knowledge and implications for the future. Tropical Medicine and Infectious Disease, 1(1), 8. https://doi.org/10.3390/tropicalmed1010008
   PubMedGoogle Scholar
• Bui, H.-H., Sidney, J., Peters, B., Sathiamurthy, M., Sinichi, A., Purton, K.-A., Mothé, B. R., Chisari, F. V., Watkins, D. I., & Sette, A. (2005). Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics, 57(5), 304–314. https://doi.org/10.1007/s00251-005-0798-y
   PubMed Web of Science ®Google Scholar
• Castiglione, F., Mantile, F., De Berardinis, P., & Prisco, A. (2012). How the interval between prime and boost injection affects the immune response in a computational model of the immune system. Computational and Mathematical Methods in Medicine, 2012, 1–9. https://doi.org/10.1155/2012/842329
   Web of Science ®Google Scholar
• Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010). MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallographica Section D, Biological Crystallography, 66(Pt 1), 12–21. https://doi.org/10.1107/S0907444909042073
   PubMed Web of Science ®Google Scholar
• DeLano, W. L. (2002). Pymol: An open-source molecular graphics tool. CCP4 Newsl. Protein Crystallogr, 40(1), 82–92.
   Google Scholar
• DeLano, W. L., & Bromberg, S. (2004). PyMOL user’s guide (p. 629). DeLano Scientific LLC.
   Google Scholar
• Desta, I. T., Porter, K. A., Xia, B., Kozakov, D., & Vajda, S. (2020). Performance and its limits in rigid body protein-protein docking. Structure (London, England: 1993), 28(9), 1071–1081. e3. https://doi.org/10.1016/j.str.2020.06.006
   PubMed Web of Science ®Google Scholar
• Dey, J., Mahapatra, S. R., Lata, S., Patro, S., Misra, N., & Suar, M. (2022). Exploring Klebsiella pneumoniae capsule polysaccharide proteins to design multiepitope subunit vaccine to fight against pneumonia. Expert Review of Vaccines, 21(4), 569–587. https://doi.org/10.1080/14760584.2022.2021882
   PubMed Web of Science ®Google Scholar
• Dey, J., Mahapatra, S. R., Patnaik, S., Lata, S., Kushwaha, G. S., Panda, R. K., Misra, N., & Suar, M. (2022). Molecular characterization and designing of a novel multiepitope vaccine construct against Pseudomonas aeruginosa. International Journal of Peptide Research and Therapeutics, 28(2), 1–19. https://doi.org/10.1007/s10989-021-10356-z
   PubMed Web of Science ®Google Scholar
• Dey, J., Mahapatra, S. R., Raj, T. K., Kaur, T., Jain, P., Tiwari, A., Patro, S., Misra, N., & Suar, M. (2022). Designing a novel multi-epitope vaccine to evoke a robust immune response against pathogenic multidrug-resistant Enterococcus faecium bacterium. Gut Pathogens, 14(1), 1–20. https://doi.org/10.1186/s13099-022-00495-z
   PubMed Web of Science ®Google Scholar
• Dimitrov, I., Bangov, I., Flower, D. R., & Doytchinova, I. (2014). AllerTOP v. 2—A server for in silico prediction of allergens. Journal of Molecular Modeling, 20(6), 1–6. https://doi.org/10.1007/s00894-014-2278-5
   Web of Science ®Google Scholar
• Doshi, R. H., Alfonso, V. H., Morier, D., Hoff, N. A., Sinai, C., Mulembakani, P., Kisalu, N., Cheng, A., Ashbaugh, H., Gadoth, A., Cowell, B., Okitolonda, E. W., Muyembe-Tamfum, J.-J., & Rimoin, A. W. (2020). Monkeypox rash severity and animal exposures in the Democratic Republic of the Congo. EcoHealth, 17(1), 64–73. https://doi.org/10.1007/s10393-019-01459-7
   PubMed Web of Science ®Google Scholar
• Doytchinova, I. A., & Flower, D. R. (2007). VaxiJen: A server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics, 8(1), 4. https://doi.org/10.1186/1471-2105-8-4
   PubMed Web of Science ®Google Scholar
• Doytchinova, I. A., & Flower, D. R. (2008). Bioinformatic approach for identifying parasite and fungal candidate subunit vaccines. Open Vaccine J, 1(1), 4.
   Google Scholar
• Dumont, C., Irenge, L. M., Magazani, E. K., Garin, D., Muyembe, J.-J T., Bentahir, M., & Gala, J.-L. (2014). Simple technique for in field samples collection in the cases of skin rash illness and subsequent PCR detection of orthopoxviruses and varicella zoster virus. PLoS One, 9(5), e96930. https://doi.org/10.1371/journal.pone.0096930
   PubMed Web of Science ®Google Scholar
• Dupuy, L. C., & Schmaljohn, C. S. (2009). DNA vaccines for biodefense. Expert Review of Vaccines, 8(12), 1739–1754. https://doi.org/10.1586/erv.09.132
   PubMed Web of Science ®Google Scholar
• Enayatkhani, M., Hasaniazad, M., Faezi, S., Gouklani, H., Davoodian, P., Ahmadi, N., Einakian, M. A., Karmostaji, A., & Ahmadi, K. (2021). Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: An in silico study. Journal of Biomolecular Structure & Dynamics, 39(8), 2857–2872. https://doi.org/10.1080/07391102.2020.1756411
   PubMed Web of Science ®Google Scholar
• Fantini, J., Chahinian, H., & Yahi, N. (2022). A vaccine strategy based on the identification of an annular ganglioside binding motif in monkeypox virus protein E8L. Viruses, 14(11), 2531. https://doi.org/10.3390/v14112531
   PubMed Web of Science ®Google Scholar
• Forbes, N., Baclic, O., Harrison, R., & Brousseau, N., The National Advisory Committee on Immunization (NACI). (2022). Summary of the National Advisory Committee on Immunization (NACI) Rapid Response: Updated interim guidance on Imvamune in the context of ongoing monkeypox outbreaks. Canada Communicable Disease Report, 48(11/12), 580–586. https://doi.org/10.14745/ccdr.v48i1112a11
   PubMedGoogle Scholar
• Franceschi, V., Parker, S., Jacca, S., Crump, R. W., Doronin, K., Hembrador, E., Pompilio, D., Tebaldi, G., Estep, R. D., Wong, S. W., Buller, M. R., & Donofrio, G. (2015). BoHV-4-based vector single heterologous antigen delivery protects STAT1 (-/-) mice from monkeypoxvirus lethal challenge. PLoS Neglected Tropical Diseases, 9(6), e0003850. https://doi.org/10.1371/journal.pntd.0003850
   PubMed Web of Science ®Google Scholar
• Friend, U. S., et al. (2009). In silico analysis of envelope Dengue Virus-2 and envelope Dengue Virus-3 protein as the backbone of Dengue Virus tetravalent vaccine by using homology modeling method. OnLine Journal of Biological Sciences, 9(1), 6–16.
   PubMedGoogle Scholar
• Garnier, J., Osguthorpe, D. J., & Robson, B. (1978). Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. Journal of Molecular Biology, 120(1), 97–120.
   PubMed Web of Science ®Google Scholar
• Gasteiger, E., et al. (2005). Protein identification and analysis tools on the ExPASy server. In The proteomics protocols handbook (pp. 571–607). Springer Protocols Handbooks. Humana Press.
   Google Scholar
• Gong, Q., Wang, C., Chuai, X., & Chiu, S. (2022). Monkeypox virus: A re-emergent threat to humans. Virologica Sinica, 37(4), 477–482. https://doi.org/10.1016/j.virs.2022.07.006
   PubMed Web of Science ®Google Scholar
• Gopalakrishnan, K., et al. (2007). Ramachandran plot on the web (2.0). Protein and Peptide Letters, 14(7), 669–671.
   PubMed Web of Science ®Google Scholar
• Gupta, S., Kapoor, P., Chaudhary, K., Gautam, A., Kumar, R., & Raghava, G. P. S., Open Source Drug Discovery Consortium. (2013). In silico approach for predicting toxicity of peptides and proteins. PLoS One, 8(9), e73957. https://doi.org/10.1371/journal.pone.0073957
   PubMed Web of Science ®Google Scholar
• Habel, J. R., Nguyen, A. T., Rowntree, L. C., Szeto, C., Mifsud, N. A., Clemens, E. B., Loh, L., Chen, W., Rockman, S., Nelson, J., Davies, J., Miller, A., Tong, S. Y. C., Rossjohn, J., Gras, S., Purcell, A. W., Hensen, L., Kedzierska, K., & Illing, P. T. (2022). HLA-A* 11: 01-restricted CD8+ T cell immunity against influenza A and influenza B viruses in Indigenous and non-Indigenous people. PLoS Pathogens, 18(3), e1010337. https://doi.org/10.1371/journal.ppat.1010337
   PubMed Web of Science ®Google Scholar
• Haider, N., Guitian, J., Simons, D., Asogun, D., Ansumana, R., Honeyborne, I., Velavan, T. P., Ntoumi, F., Valdoleiros, S. R., Petersen, E., Kock, R., & Zumla, A. (2022). Increased outbreaks of monkeypox highlight gaps in actual disease burden in Sub-Saharan Africa and in animal reservoirs. International Journal of Infectious Diseases, 122, 107–111. https://doi.org/10.1016/j.ijid.2022.05.058
   PubMed Web of Science ®Google Scholar
• Hraib, M., Jouni, S., Albitar, M. M., Alaidi, S., & Alshehabi, Z. (2022). The outbreak of monkeypox 2022: An overview. Annals of Medicine & Surgery, 79, 104069. https://doi.org/10.1016/j.amsu.2022.104069
   PubMed Web of Science ®Google Scholar
• Huang, Y., Mu, L., & Wang, W. (2022). Monkeypox: Epidemiology, pathogenesis, treatment and prevention. Signal Transduction and Targeted Therapy, 7(1), 1–22. https://doi.org/10.1038/s41392-022-01215-4
   PubMed Web of Science ®Google Scholar
• Isidro, J., Borges, V., Pinto, M., Sobral, D., Santos, J. D., Nunes, A., Mixão, V., Ferreira, R., Santos, D., Duarte, S., Vieira, L., Borrego, M. J., Núncio, S., de Carvalho, I. L., Pelerito, A., Cordeiro, R., & Gomes, J. P. (2022). Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus. Nature Medicine, 28(10), 2220–2221. https://doi.org/10.1038/s41591-022-02036-2
   PubMed Web of Science ®Google Scholar
• Jahantigh, H. R., Stufano, A., Lovreglio, P., Rezaee, S. A., & Ahmadi, K. (2022). In silico identification of epitope-based vaccine candidates against HTLV-1. Journal of Biomolecular Structure & Dynamics, 40(15), 6737–6754. https://doi.org/10.1080/07391102.2021.1889669
   PubMed Web of Science ®Google Scholar
• Keckler, M. S., Salzer, J. S., Patel, N., Townsend, M. B., Nakazawa, Y. J., Doty, J. B., Gallardo-Romero, N. F., Satheshkumar, P. S., Carroll, D. S., Karem, K. L., & Damon, I. K. (2020). IMVAMUNE® and ACAM2000® provide different protection against disease when administered postexposure in an intranasal monkeypox challenge prairie dog model. Vaccines, 8(3), 396. https://doi.org/10.3390/vaccines8030396
   PubMed Web of Science ®Google Scholar
• Khan, M. N., & Pichichero, M. E. (2014). The host immune dynamics of pneumococcal colonization: Implications for novel vaccine development. Human Vaccines & Immunotherapeutics, 10(12), 3688–3699. https://doi.org/10.4161/21645515.2014.979631
   PubMed Web of Science ®Google Scholar
• Kugelman, J. R., Johnston, S. C., Mulembakani, P. M., Kisalu, N., Lee, M. S., Koroleva, G., McCarthy, S. E., Gestole, M. C., Wolfe, N. D., Fair, J. N., Schneider, B. S., Wright, L. L., Huggins, J., Whitehouse, C. A., Wemakoy, E. O., Muyembe-Tamfum, J. J., Hensley, L. E., Palacios, G. F., & Rimoin, A. W. (2014). Genomic variability of monkeypox virus among humans, Democratic Republic of the Congo. Emerging Infectious Diseases, 20(2), 232–239. https://doi.org/10.3201/eid2002.130118
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A., Open Source Drug Discovery Consortium. (2014). g_mmpbsa—A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Li, D., Wilkins, K., McCollum, A. M., Osadebe, L., Kabamba, J., Nguete, B., Likafi, T., Balilo, M. P., Lushima, R. S., Malekani, J., Damon, I. K., Vickery, M. C. L., Pukuta, E., Nkawa, F., Karhemere, S., Tamfum, J.-J M., Okitolonda, E. W., Li, Y., & Reynolds, M. G. (2017). Evaluation of the GeneXpert for human monkeypox diagnosis. The American Journal of Tropical Medicine and Hygiene, 96(2), 405–410. https://doi.org/10.4269/ajtmh.16-0567
   PubMed Web of Science ®Google Scholar
• Likitlersuang, J., Koh, R., Gong, X., Jovanovic, L., Bolivar-Tellería, I., Myers, M., Zariffa, J., & Márquez-Chin, C. (2018). EEG-controlled functional electrical stimulation therapy with automated grasp selection: A proof-of-concept study. Topics in Spinal Cord Injury Rehabilitation, 24(3), 265–274. https://doi.org/10.1310/sci2403-265
   PubMed Web of Science ®Google Scholar
• Liljeroos, L., Malito, E., Ferlenghi, I., & Bottomley, M. J. (2015). Structural and computational biology in the design of immunogenic vaccine antigens. Journal of Immunology Research, 2015, 1–17. https://doi.org/10.1155/2015/156241
   PubMed Web of Science ®Google Scholar
• Lozano, J. M., & Muller, S. (2023). Monkeypox: Potential vaccine development strategies. Trends in Pharmacological Sciences, 44(1), 15–19. https://doi.org/10.1016/j.tips.2022.10.005
   PubMed Web of Science ®Google Scholar
• Mahapatra, S. R., Dey, J., Raj, T. K., Kumar, V., Ghosh, M., Verma, K. K., Kaur, T., Kesawat, M. S., Misra, N., & Suar, M. (2022). The potential of plant-derived secondary metabolites as novel drug candidate against Klebsiella pneumoniae: Molecular docking and simulation investigation. South African Journal of Botany, 149, 789–797. https://doi.org/10.1016/j.sajb.2022.04.043
   PubMed Web of Science ®Google Scholar
• Manici, S., Sturniolo, T., Imro, M. A., Hammer, J., Sinigaglia, F., Noppen, C., Spagnoli, G., Mazzi, B., Bellone, M., Dellabona, P., & Protti, M. P. (1999). Melanoma cells present a MAGE-3 epitope to CD4+ cytotoxic T cells in association with histocompatibility leukocyte antigen DR11. The Journal of Experimental Medicine, 189(5), 871–876. https://doi.org/10.1084/jem.189.5.871
   PubMed Web of Science ®Google Scholar
• Martínez, J. I., et al. (2022). Monkeypox outbreak predominantly affecting men who have sex with men, Madrid, Spain, 26 April to 16 June 2022. Eurosurveillance, 27(27), 2200471.
   Google Scholar
• McInnes, C. J., Wood, A. R., Thomas, K., Sainsbury, A. W., Gurnell, J., Dein, F. J., & Nettleton, P. F. (2006). Genomic characterization of a novel poxvirus contributing to the decline of the red squirrel (Sciurus vulgaris) in the UK. The Journal of General Virology, 87(Pt 8), 2115–2125. https://doi.org/10.1099/vir.0.81966-0
   PubMedGoogle Scholar
• Meo, S. A., Al-Masri, A. A., Klonoff, D. C., Alshahrani, A. N., & Al-Khlaiwi, T. (2022). Comparison of Biological, Pharmacological Characteristics, Indications, Contraindications and Adverse Effects of JYNNEOS and ACAM2000 Monkeypox Vaccines. Vaccines, 10(11), 1971. https://doi.org/10.3390/vaccines10111971
   PubMed Web of Science ®Google Scholar
• Meyer, H., Totmenin, A., Gavrilova, E., & Shchelkunov, S. (2005). Variola and camelpox virus-specific sequences are part of a single large open reading frame identified in two German cowpox virus strains. Virus Research, 108(1-2), 39–43. https://doi.org/10.1016/j.virusres.2004.07.011
   PubMed Web of Science ®Google Scholar
• Mobini, S., Chizari, M., Mafakher, L., Rismani, E., & Rismani, E. (2020). Computational design of a novel VLP-based vaccine for hepatitis B virus. Frontiers in Immunology, 11, 2074. https://doi.org/10.3389/fimmu.2020.02074
   PubMed Web of Science ®Google Scholar
• Narang, P. K., Dey, J., Mahapatra, S. R., Ghosh, M., Misra, N., Suar, M., Kumar, V., & Raina, V. (2021). Functional annotation and sequence-structure characterization of a hypothetical protein putatively involved in carotenoid biosynthesis in microalgae. South African Journal of Botany, 141, 219–226. https://doi.org/10.1016/j.sajb.2021.04.014
   Web of Science ®Google Scholar
• Nielsen, M., Lundegaard, C., & Lund, O. (2007). Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics, 8(1), 238. https://doi.org/10.1186/1471-2105-8-238
   PubMed Web of Science ®Google Scholar
• Nielsen, M., Lundegaard, C., Worning, P., Lauemøller, S. L., Lamberth, K., Buus, S., Brunak, S., & Lund, O. (2003). Reliable prediction of T‐cell epitopes using neural networks with novel sequence representations. Protein Science, 12(5), 1007–1017. https://doi.org/10.1110/ps.0239403
   PubMed Web of Science ®Google Scholar
• Niwa, T., Ying, B.-W., Saito, K., Jin, W., Takada, S., Ueda, T., & Taguchi, H. (2009). Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins. Proceedings of the National Academy of Sciences of the United States of America, 106(11), 4201–4206. https://doi.org/10.1073/pnas.0811922106
   PubMed Web of Science ®Google Scholar
• Ogoina, D., & Yinka-Ogunleye, A. (2022). Sexual history of human monkeypox patients seen at a tertiary hospital in Bayelsa, Nigeria. International Journal of STD & AIDS, 33(10), 928–932. https://doi.org/10.1177/09564624221119335
   PubMed Web of Science ®Google Scholar
• Orviz, E., Negredo, A., Ayerdi, O., Vázquez, A., Muñoz-Gomez, A., Monzón, S., Clavo, P., Zaballos, A., Vera, M., Sánchez, P., Cabello, N., Jiménez, P., Pérez-García, J. A., Varona, S., del Romero, J., Cuesta, I., Delgado-Iribarren, A., Torres, M., Sagastagoitia, I., … Zarza, I. (2022). Monkeypox outbreak in Madrid (Spain): Clinical and virological aspects. Journal of Infection, 85(4), 412–417. https://doi.org/10.1016/j.jinf.2022.07.005
   PubMed Web of Science ®Google Scholar
• Petersen, B. W., Kabamba, J., McCollum, A. M., Lushima, R. S., Wemakoy, E. O., Muyembe Tamfum, J.-J., Nguete, B., Hughes, C. M., Monroe, B. P., & Reynolds, M. G. (2019). Vaccinating against monkeypox in the Democratic Republic of the Congo. Antiviral Research, 162, 171–177. https://doi.org/10.1016/j.antiviral.2018.11.004
   PubMed Web of Science ®Google Scholar
• Petersen, E., Zumla, A., Hui, D. S., Blumberg, L., Valdoleiros, S. R., Amao, L., Ntoumi, F., Asogun, D., Simonsen, L., Haider, N., Traore, T., Kapata, N., Dar, O., Nachega, J., Abbara, A., Al Balushi, A., Kock, R., Maeurer, M., Lee, S. S., … Koopmans, M. (2022). Vaccination for monkeypox prevention in persons with high-risk sexual behaviours to control on-going outbreak of monkeypox virus clade 3. International Journal of Infectious Diseases: IJID, 122, 569–571. https://doi.org/10.1016/j.ijid.2022.06.047
   PubMed Web of Science ®Google Scholar
• Poland, G. A., Ovsyannikova, I. G., & Kennedy, R. B. (2018). Personalized vaccinology: A review. Vaccine, 36(36), 5350–5357. https://doi.org/10.1016/j.vaccine.2017.07.062
   PubMed Web of Science ®Google Scholar
• Ponomarenko, J. V., & Bourne, P. E. (2007). Antibody-protein interactions: Benchmark datasets and prediction tools evaluation. BMC Structural Biology, 7(1), 64. https://doi.org/10.1186/1472-6807-7-64
   PubMedGoogle Scholar
• Ponomarenko, J., Bui, H.-H., Li, W., Fusseder, N., Bourne, P. E., Sette, A., & Peters, B. (2008). ElliPro: A new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics, 9(1), 1–8. https://doi.org/10.1186/1471-2105-9-514
   PubMedGoogle Scholar
• Rapin, N., Lund, O., Bernaschi, M., & 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(4), e9862. https://doi.org/10.1371/journal.pone.0009862
   PubMed Web of Science ®Google Scholar
• Sah, R., Abdelaal, A., Reda, A., Katamesh, B. E., Manirambona, E., Abdelmonem, H., Mehta, R., Rabaan, A. A., Alhumaid, S., Alfouzan, W. A., Alomar, A. I., Khamis, F., Alofi, F. S., Aljohani, M. H., Alfaraj, A. H., Alfaresi, M., Al-Jishi, J. M., Alsalman, J., Alynbiawi, A., Almogbel, M. S., & Rodriguez-Morales, A. J. (2022). Monkeypox and its Possible Sexual Transmission: Where are we now with its evidence? Pathogens, 11(8), 924. https://doi.org/10.3390/pathogens11080924
   PubMed Web of Science ®Google Scholar
• Saha, S., & Raghava, G. P. S. (2006). Prediction of continuous B‐cell epitopes in an antigen using recurrent neural network. Proteins, 65(1), 40–48. https://doi.org/10.1002/prot.21078
   PubMed Web of Science ®Google Scholar
• Sahoo, P., Dey, J., Mahapatra, S. R., Ghosh, A., Jaiswal, A., Padhi, S., Prabhuswamimath, S. C., Misra, N., & Suar, M. (2022). Nanotechnology and COVID-19 convergence: Toward new planetary health interventions against the pandemic. Omics, 26(9), 473–488. https://doi.org/10.1089/omi.2022.0072
   PubMed Web of Science ®Google Scholar
• Saijo, M., Ami, Y., Suzaki, Y., Nagata, N., Iwata, N., Hasegawa, H., Ogata, M., Fukushi, S., Mizutani, T., Sata, T., Kurata, T., Kurane, I., & Morikawa, S. (2006). LC16m8, a highly attenuated vaccinia virus vaccine lacking expression of the membrane protein B5R, protects monkeys from monkeypox. Journal of Virology, 80(11), 5179–5188. https://doi.org/10.1128/JVI.02642-05
   PubMed Web of Science ®Google Scholar
• Shin, W.-H., et al. (2014). Prediction of protein structure and interaction by GALAXY protein modeling programs. Bio Design, 2(1), 1–11.
   Google Scholar
• Silva, M. S. T., et al. (2022). Ambulatory and hospitalized patients with suspected and confirmed mpox: An observational cohort study from Brazil. The Lancet Regional Health-Americas, 17, 100406.
   PubMedGoogle Scholar
• Singh, H., & Raghava, G. (2001). ProPred: Prediction of HLA-DR binding sites. Bioinformatics (Oxford, England), 17(12), 1236–1237. https://doi.org/10.1093/bioinformatics/17.12.1236
   PubMed Web of Science ®Google Scholar
• Singh, R., et al. (2020). Unsupervised manifold alignment for single-cell multi-omics data. Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. https://doi.org/10.1145/3388440.3412410
   Google Scholar
• Soleymani, S., Tavassoli, A., & Housaindokht, M. R. (2021). An overview of progress from empirical to rational design in modern vaccine development, with an emphasis on computational tools and immunoinformatics approaches. Computers in Biology and Medicine, 140, 105057. https://doi.org/10.1016/j.compbiomed.2021.105057
   PubMed Web of Science ®Google Scholar
• Townsend, M. B., Gallardo-Romero, N. F., Khmaladze, E., Vora, N. M., Maghlakelidze, G., Geleishvili, M., Carroll, D. S., Emerson, G. L., Reynolds, M. G., & Satheshkumar, P. S. (2017). Retrospective proteomic analysis of serum after Akhmeta virus infection: New suspect case identification and insights into poxvirus humoral immunity. The Journal of Infectious Diseases, 216(12), 1505–1512. https://doi.org/10.1093/infdis/jix534
   PubMed Web of Science ®Google Scholar
• Van Regenmortel, M. H. (2016). Structure-based reverse vaccinology failed in the case of HIV because it disregarded accepted immunological theory. International Journal of Molecular Sciences, 17(9), 1591. https://doi.org/10.3390/ijms17091591
   PubMed Web of Science ®Google Scholar
• Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, 8(2), 127–134. https://doi.org/10.1093/protein/8.2.127
   PubMedGoogle Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server issue), W407–W410. https://doi.org/10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar