Designing a multi-epitope candidate vaccine by employing immunoinformatics approaches to control African swine fever spread

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Affairs, M. O A. F. A., R. (2022). ASF - Information of current status of occurrences, https://www.mafra.go.kr/FMD-AI2/2145/subview.do.
   Google Scholar
• Akhtar, N., Joshi, A., Kaushik, V., Kumar, M., & Mannan, M. A.-u. (2021a). In-silico design of a multivalent epitope-based vaccine against Candida auris. Microbial Pathogenesis, 155, 104879. https://doi.org/10.1016/j.micpath.2021.104879
   PubMed Web of Science ®Google Scholar
• Akhtar, N., Joshi, A., Singh, J., & Kaushik, V. (2021b). Design of a novel and potent multivalent epitope based human cytomegalovirus peptide vaccine: An immunoinformatics approach. Journal of Molecular Liquids, 335, 116586. https://doi.org/10.1016/j.molliq.2021.116586
   Web of Science ®Google Scholar
• Ali, M., Pandey, R. K., Khatoon, N., Narula, A., Mishra, A., & Prajapati, V. K. (2017). Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection. Scientific Reports, 7(9232), 1-13. https://doi.org/10.1038/s41598-017-09199-w
   Google Scholar
• Bajusz, D., Rácz, A., & Héberger, K. (2015). Why is Tanimoto index an appropriate choice for fingerprint-based similarity calculations? Journal of Cheminformatics, 7(1), 20–20. https://doi.org/10.1186/s13321-015-0069-3
   PubMedGoogle Scholar
• Bech-Nielsen, S., Fernandez, J., Martinez-Pereda, F., Espinosa, J., Perez Bonilla, Q., & Sanchez-Vizcaino, J. M. (1995). A case study of an outbreak of African swine fever in Spain. The British Veterinary Journal, 151(2), 203–214. https://doi.org/10.1016/s0007-1935(95)80012-3
   PubMedGoogle Scholar
• Bibi, S., Ullah, I., Zhu, B., Adnan, M., Liaqat, R., Kong, W.-B., & Niu, S. (2021). In silico analysis of epitope-based vaccine candidate against tuberculosis using reverse vaccinology. Scientific Reports, 11(1249), 1-16. https://doi.org/10.1038/s41598-020-80899-6
   Google Scholar
• Blome, S., Gabriel, C., & Beer, M. (2014). Modern adjuvants do not enhance the efficacy of an inactivated African swine fever virus vaccine preparation. Vaccine, 32(31), 3879–3882. https://doi.org/10.1016/j.vaccine.2014.05.051
   PubMed Web of Science ®Google Scholar
• Breese, S. S., Stone, S. S., Deboer, C. J., & Hess, W. R. (1967). Electron microscopy of the interaction of African swine fever virus with ferritin-conjugated antibody. Virology, 31(3), 508–513. https://doi.org/10.1016/0042-6822(67)90232-2
   PubMed Web of Science ®Google Scholar
• Buchan, D., W., A., Minneci, F., Nugent, T. C. O., Bryson, K., & Jones, D. T. (2013). Scalable web services for the PSIPRED Protein Analysis Workbench. Nucleic Acids Research, 41(Web Server issue), W349–W357. https://doi.org/10.1093/nar/gkt381
   PubMed Web of Science ®Google Scholar
• Burmakina, G., Malogolovkin, A., Tulman, E. R., Xu, W., Delhon, G., Kolbasov, D., & Rock, D. L. (2019). Identification of T-cell epitopes in African swine fever virus CD2v and C-type lectin proteins. The Journal of General Virology, 100(2), 259–265. https://doi.org/10.1099/jgv.0.001195
   PubMed Web of Science ®Google Scholar
• Chauhan, V., Rungta, T., Goyal, K., & Singh, M. P. (2019). Designing a multi-epitope based vaccine to combat Kaposi Sarcoma utilizing immunoinformatics approach. Scientific Reports, 9(1), 2517–2517. https://doi.org/10.1038/s41598-019-39299-8
   PubMedGoogle Scholar
• Chawla, M., Abdel-Azeim, S., Oliva, R., & Cavallo, L. (2014). Higher order structural effects stabilizing the reverse Watson-Crick Guanine-Cytosine base pair in functional RNAs. Nucleic Acids Research, 42(2), 714–726. https://doi.org/10.1093/nar/gkt800
   PubMed Web of Science ®Google Scholar
• Chawla, M., Credendino, R., Oliva, R., & Cavallo, L. (2015a). Structural and energetic impact of non-natural 7-Deaza-8-Azaadenine and its 7-substituted derivatives on H-bonding potential with uracil in RNA molecules. The Journal of Physical Chemistry. B, 119(41), 12982–12989. https://doi.org/10.1021/acs.jpcb.5b06861
   PubMed Web of Science ®Google Scholar
• Chawla, M., Credendino, R., Poater, A., Oliva, R., & Cavallo, L. (2015b). Structural stability, acidity, and halide selectivity of the fluoride Riboswitch recognition site. Journal of the American Chemical Society, 137(1), 299–306. https://doi.org/10.1021/ja510549b
   PubMed Web of Science ®Google Scholar
• Chawla, M., Gorle, S., Shaikh, A. R., Oliva, R., & Cavallo, L. (2021). Replacing thymine with a strongly pairing fifth Base: A combined quantum mechanics and molecular dynamics study. Computational and Structural Biotechnology Journal, 19, 1312–1324. https://doi.org/10.1016/j.csbj.2021.02.006
   PubMed Web of Science ®Google Scholar
• Chawla, M., Oliva, R., Bujnicki, J. M., & Cavallo, L. (2015c). An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies. Nucleic Acids Research, 43(14), 6714–6729. https://doi.org/10.1093/nar/gkv606
   PubMed Web of Science ®Google Scholar
• Chawla, M., Poater, A., Besalú-Sala, P., Kalra, K., Oliva, R., & Cavallo, L. (2018). Theoretical characterization of sulfur-to-selenium substitution in an emissive RNA alphabet: Impact on H-bonding potential and photophysical properties. Physical Chemistry Chemical Physics : PCCP, 20(11), 7676–7685. https://doi.org/10.1039/c7cp07656h
   PubMed Web of Science ®Google Scholar
• Costard, S., Wieland, B., de Glanville, W., Jori, F., Rowlands, R., Vosloo, W., Roger, F., Pfeiffer, D. U., & Dixon, L. K. (2009). African swine fever: How can global spread be prevented? Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 364(1530), 2683–2696. https://doi.org/10.1098/rstb.2009.0098
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: AnN⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Dimitrov, I., Naneva, L., Doytchinova, I., & Bangov, I. (2014). AllergenFP: Allergenicity prediction by descriptor fingerprints. Bioinformatics (Oxford, England), 30(6), 846–851. https://doi.org/10.1093/bioinformatics/btt619
   PubMed Web of Science ®Google Scholar
• Dixon, L. K., Chapman, D. A. G., Netherton, C. L., & Upton, C. (2013). African swine fever virus replication and genomics. Virus Research, 173(1), 3–14. https://doi.org/10.1016/j.virusres.2012.10.020
   PubMed Web of Science ®Google Scholar
• Domínguez, M. A., Landi, V., Martínez, A., & Garrido, J. J. (2014). Identification and functional characterization of novel genetic variations in Porcine TLR5 promoter. DNA and Cell Biology, 33(7), 469–476. https://doi.org/10.1089/dna.2013.2318
   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), 4–4. https://doi.org/10.1186/1471-2105-8-4
   PubMed Web of Science ®Google Scholar
• Eustace Montgomery, R. (1921). On a form of Swine Fever occurring in British East Africa (Kenya Colony). Journal of Comparative Pathology and Therapeutics, 34, 159–191. https://doi.org/10.1016/s0368-1742(21)80031-4
   Google Scholar
• Faber, E., Tedin, K., Speidel, Y., Brinkmann, M. M., & Josenhans, C. (2018). Functional expression of TLR5 of different vertebrate species and diversification in intestinal pathogen recognition. Scientific Reports, 8(11287), 1-16. https://doi.org/10.1038/s41598-018-29371-0
   Google Scholar
• Flamme, M., Röthlisberger, P., Levi-Acobas, F., Chawla, M., Oliva, R., Cavallo, L., Gasser, G., Marlière, P., Herdewijn, P., & Hollenstein, M. (2020). Enzymatic formation of an artificial base pair using a modified purine nucleoside triphosphate. ACS Chemical Biology, 15(11), 2872–2884. https://doi.org/10.1021/acschembio.0c00396
   PubMed Web of Science ®Google Scholar
• Galindo, I., & Alonso, C. (2017). African Swine Fever Virus: A review. Viruses, 9(5), 103. https://doi.org/10.3390/v9050103
   PubMed Web of Science ®Google Scholar
• Gasteiger, E. (2005). The proteomics protocols handbook (pp. 571–607). Humana Press.
   Google Scholar
• Gogin, A., Gerasimov, V., Malogolovkin, A., & Kolbasov, D. (2013). African swine fever in the North Caucasus region and the Russian Federation in years 2007–2012. Virus Research, 173(1), 198–203. https://doi.org/10.1016/j.virusres.2012.12.007
   PubMed Web of Science ®Google Scholar
• Gómez-Puertas, P., Rodríguez, F., Oviedo, J. M., Brun, A., Alonso, C., & Escribano, J. M. (1998). The African Swine fever virus proteins p54 and p30 are involved in two distinct steps of virus attachment and both contribute to the antibody-mediated protective immune Response. Virology, 243(2), 461–471. https://doi.org/10.1006/viro.1998.9068
   PubMed Web of Science ®Google Scholar
• Gómez-Puertas, P., Rodríguez, F., Oviedo, J. M., Ramiro-Ibáñez, F., Ruiz-Gonzalvo, F., Alonso, C., & Escribano, J. M. (1996). Neutralizing antibodies to different proteins of African swine fever virus inhibit both virus attachment and internalization. Journal of Virology, 70(8), 5689–5694. https://doi.org/10.1128/JVI.70.8.5689-5694.1996
   PubMed Web of Science ®Google Scholar
• Gonzalez, H. C., Darré, L., & Pantano, S. (2013). Transferable mixing of atomistic and coarse-grained water models. The Journal of Physical Chemistry. B, 117(46), 14438–14448. https://doi.org/10.1021/jp4079579
   PubMed Web of Science ®Google Scholar
• Grewal, R. K., Shaikh, A. R., Gorle, S., Kaur, M., Videira, P. A., Cavallo, L., & Chawla, M. (2021). Structural insights in mammalian sialyltransferases and fucosyltransferases: We have come a long way, but it is still a long way down. Molecules, 26(17), 5203. https://doi.org/10.3390/molecules26175203
   PubMed Web of Science ®Google Scholar
• Grote, A., Hiller, K., Scheer, M., Münch, R., Nörtemann, B., Hempel, D. C., & Jahn, D. (2005). JCat: a novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Research, 33(Web Server issue), W526–W531. https://doi.org/10.1093/nar/gki376
   PubMed Web of Science ®Google Scholar
• Hajighahramani, N., Nezafat, N., Eslami, M., Negahdaripour, M., Rahmatabadi, S. S., & Ghasemi, Y. (2017). Immunoinformatics analysis and in silico designing of a novel multi-epitope peptide vaccine against Staphylococcus aureus. Infection, Genetics and Evolution, 48, 83–94. https://doi.org/10.1016/j.meegid.2016.12.010
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H., J., C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(sici)1096-987x(199709)18:12<1463::aid-jcc4>3.0.co;2-h
   Web of Science ®Google Scholar
• Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., de Groot, B. L., Grubmüller, H., & MacKerell, A. D. (2017). CHARMM36m: An improved force field for folded and intrinsically disordered proteins. Nature Methods, 14(1), 71–73. https://doi.org/10.1038/nmeth.4067
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Ichiye, T., & Karplus, M. (1991). Collective motions in proteins: A co-variance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins, 11(3), 205–217. https://doi.org/10.1002/prot.340110305
   PubMed Web of Science ®Google Scholar
• Ikai, A. (1980). Thermostability and aliphatic index of globular proteins. The Journal of Biochemistry, 88, 1895–1898. https://doi.org/10.1093/oxfordjournals.jbchem.a133168
   PubMed Web of Science ®Google Scholar
• Jain, P., Joshi, A., Akhtar, N., Krishnan, S., & Kaushik, V. (2021). An immunoinformatics study: designing multivalent T-cell epitope vaccine against canine circovirus. Journal, Genetic Engineering & Biotechnology, 19(1), 121–121. https://doi.org/10.1186/s43141-021-00220-4
   PubMed Web of Science ®Google Scholar
• Jespersen, M. C., Peters, B., Nielsen, M., & Marcatili, P. (2017). BepiPred-2.0: Improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Research, 45(W1), W24–W29. https://doi.org/10.1093/nar/gkx346
   PubMed Web of Science ®Google Scholar
• Jia, N., Ou, Y., Pejsak, Z., Zhang, Y., & Zhang, J. (2017). Roles of African Swine Fever virus structural proteins in viral infection. Journal of Veterinary Research, 61(2), 135–143. https://doi.org/10.1515/jvetres-2017-0017
   PubMed Web of Science ®Google Scholar
• Joshi, A., & Kaushik, V. (2021). Silico proteomic exploratory quest: Crafting T-cell epitope vaccine against Whipple’s Disease. International Journal of Peptide Research and Therapeutics, 27(1), 169–179. https://doi.org/10.1007/s10989-020-10077-9
   PubMed Web of Science ®Google Scholar
• Joshi, A., Pathak, D. C., Mannan, M. A.-U., & Kaushik, V. (2021). In-silico designing of epitope-based vaccine against the seven banded grouper nervous necrosis virus affecting fish species. Network Modeling and Analysis in Health Informatics and Bioinformatics, 10(1), 37–37. https://doi.org/10.1007/s13721-021-00315-5
   PubMed Web of Science ®Google Scholar
• Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., … Hassabis, D. (2021). Highly accurate protein structure prediction with AlphaFold. Nature, 596(7873), 583–589. https://doi.org/10.1038/s41586-021-03819-2
   PubMed Web of Science ®Google Scholar
• Kabra, A., Mukim, M., Uddin, K., Kabra, R., & Kukkar, R. (2020). African Swine Fever: An emerging viral disease in India – A review. Journal of Biological and Chemical Chronicles, 6(1), 10–18. https://doi.org/10.33980/jbcc.2020.v06i01.003
   Google Scholar
• Kalra, K., Gorle, S., Cavallo, L., Oliva, R., & Chawla, M. (2020). Occurrence and stability of lone pair-π and OH-π interactions between water and nucleobases in functional RNAs. Nucleic Acids Research, 48(11), 5825–5838. https://doi.org/10.1093/nar/gkaa345
   PubMed Web of Science ®Google Scholar
• Karplus, M., & Kuriyan, J. (2005). Molecular dynamics and protein function. Proceedings of the National Academy of Sciences of the United States of America, 102(19), 6679–6685. https://doi.org/10.1073/pnas.0408930102
   PubMed Web of Science ®Google Scholar
• Kaushik, V., Jain, P., Akhtar, N., Joshi, A., Gupta, L. R., Grewal, R. K., Oliva, R., Shaikh, A. R., Cavallo, L., & Chawla, M. (2022b). Immunoinformatics-aided design and in vivo validation of a peptide-based multiepitope vaccine targeting canine circovirus. ACS Pharmacology & Translational Science, 5(8), 679–691. https://doi.org/10.1021/acsptsci.2c00130
   Google Scholar
• Kaushik, V., Krishnan, S. G., Gupta, L. R., Kalra, U., Shaikh, A. R., Cavallo, L., & Chawla, M. (2022a). Immunoinformatics aided design and in-vivo validation of a cross-reactive peptide based multi-epitope vaccine targeting multiple serotypes of dengue virus. Frontiers in Immunology, 13(865180), 1-12. https://doi.org/10.3389/fimmu.2022.865180
   Web of Science ®Google Scholar
• Khim, K., Bang, Y. J., Puth, S., Choi, Y., Lee, Y. S., Jeong, K., Lee, S. E., & Rhee, J. H. (2021). Deimmunization of flagellin for repeated administration as a vaccine adjuvant. Npj Vaccines, 6(116), 1-14. https://doi.org/10.1038/s41541-021-00379-4
   PubMedGoogle Scholar
• Lacasta, A., Ballester, M., Monteagudo, P. L., Rodríguez, J. M., Salas, M. L., Accensi, F., Pina-Pedrero, S., Bensaid, A., Argilaguet, J., López-Soria, S., Hutet, E., Le Potier, M. F., & Rodríguez, F. (2014). Expression library immunization can confer protection against lethal challenge with African swine fever virus. Journal of Virology, 88(22), 13322–13332. https://doi.org/10.1128/JVI.01893-14
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., Rullmannn, J. A., MacArthur, M. W., Kaptein, R., & Thornton, J. M. (1996). AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. Journal of Biomolecular NMR, 8(4), 477–486. https://doi.org/10.1007/bf00228148
   PubMed Web of Science ®Google Scholar
• Laskowski, R., Rullmann, J. A., Macarthur, M., Kaptein, R., & Thornton, J. (1996). AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. Journal of Biomolecular NMR, 8(4), 477-486. https://doi.org/10.1007/bf00228148
   PubMed Web of Science ®Google Scholar
• López-Blanco, J. R., Aliaga, J. I., Quintana-Ortí, E. S., & Chacón, P. (2014). iMODS: Internal coordinates normal mode analysis server. Nucleic Acids Research, 42(Web Server issue), W271–W276. https://doi.org/10.1093/nar/gku339
   PubMed Web of Science ®Google Scholar
• López-Otín, C., Freije, J. M. P., Parra, F., Mendez, E., & Viñuela, E. (1990). Mapping and sequence of the gene coding for protein p72, the major capsid protein of African swine fever virus. Virology, 175(2), 477–484. https://doi.org/10.1016/0042-6822(90)90432-q
   PubMed Web of Science ®Google Scholar
• Machado, M. R., Barrera, E. E., Klein, F., Sóñora, M., Silva, S., & Pantano, S. (2019). The SIRAH 2.0 Force Field: Altius, Fortius, Citius. Journal of Chemical Theory and Computation, 15(4), 2719–2733. https://doi.org/10.1021/acs.jctc.9b00006
   PubMed Web of Science ®Google Scholar
• Mebus, C. A. (1988). Advances in Virus Research (pp. 251–269). Elsevier.
   Google Scholar
• Mima, K. A., Katorkina, E. I., Katorkin, S. A., Tsybanov, S. Z., & Malogolovkin, A. S. (2020). In silico prediction of B- and T-cell epitopes in the CD2v protein of African swine fever virus (African swine fever virus, Asfivirus, Asfarviridae). Problems of Virology (Voprosy Virusologii), 65(2), 103–112. https://doi.org/10.36233/0507-4088-2020-65-2-103-112
   Google Scholar
• Mirdita, M., Ovchinnikov, S., & Steinegger, M. (2021). ColabFold - Making protein folding accessible to all. Cold Spring Harbor Laboratory.
   Google Scholar
• Moutaftsi, M., Peters, B., Pasquetto, V., Tscharke, D. C., Sidney, J., Bui, H.-H., Grey, H., & Sette, A. (2006). A consensus epitope prediction approach identifies the breadth of murine TCD8+-cell responses to vaccinia virus. Nature Biotechnology, 24(7), 817–819. https://doi.org/10.1038/nbt1215
   PubMed Web of Science ®Google Scholar
• Negahdaripour, M., Nezafat, N., Eslami, M., Ghoshoon, M. B., Shoolian, E., Najafipour, S., Morowvat, M. H., Dehshahri, A., Erfani, N., & Ghasemi, Y. (2018). Structural vaccinology considerations for in silico designing of a multi-epitope vaccine. Infection, Genetics and Evolution, 58, 96–109. https://doi.org/10.1016/j.meegid.2017.12.008
   PubMed Web of Science ®Google Scholar
• Neilan, J. G., Zsak, L., Lu, Z., Burrage, T. G., Kutish, G. F., & Rock, D. L. (2004). Neutralizing antibodies to African swine fever virus proteins p30, p54, and p72 are not sufficient for antibody-mediated protection. Virology, 319(2), 337–342. https://doi.org/10.1016/j.virol.2003.11.011
   PubMed Web of Science ®Google Scholar
• Netherton, C. L., & Wileman, T. E. (2013). African swine fever virus organelle rearrangements. Virus Research, 173(1), 76–86. https://doi.org/10.1016/j.virusres.2012.12.014
   PubMed Web of Science ®Google Scholar
• Nguyen, T. L., Lee, Y., & Kim, H. (2022). Immunogenic epitope-based vaccine prediction from surface glycoprotein of MERS-CoV by deploying immunoinformatics approach. International Journal of Peptide Research and Therapeutics, 28(77), 1-11. https://doi.org/10.1007/s10989-022-10382-5
   PubMedGoogle Scholar
• O'Donnell, V., Holinka, L. G., Gladue, D. P., Sanford, B., Krug, P. W., Lu, X., Arzt, J., Reese, B., Carrillo, C., Risatti, G. R., & Borca, M. V. (2015a). African Swine Fever Virus Georgia Isolate Harboring Deletions of MGF360 and MGF505 genes is attenuated in swine and confers protection against challenge with virulent parental virus. Journal of Virology, 89(11), 6048–6056. https://doi.org/10.1128/JVI.00554-15
   PubMed Web of Science ®Google Scholar
• O'Donnell, V., Holinka, L. G., Krug, P. W., Gladue, D. P., Carlson, J., Sanford, B., Alfano, M., Kramer, E., Lu, Z., Arzt, J., Reese, B., Carrillo, C., Risatti, G. R., & Borca, M. V. (2015b). African Swine Fever Virus Georgia 2007 with a deletion of virulence-associated gene 9GL (B119L), when administered at low doses, leads to virus attenuation in swine and induces an effective protection against homologous challenge. Journal of Virology, 89(16), 8556–8566. https://doi.org/10.1128/JVI.00969-15
   PubMed Web of Science ®Google Scholar
• Oliva, R., Shaikh, A. R., Petta, A., Vangone, A., & Cavallo, L. (2021). D936Y and other mutations in the fusion core of the SARS-CoV-2 spike protein heptad repeat 1: Frequency, geographical distribution, and structural effect. Molecules, 26(9), 2622. https://doi.org/10.3390/molecules26092622
   PubMed Web of Science ®Google Scholar
• Oyarzun, P., Ellis, J. J., Gonzalez-Galarza, F. F., Jones, A. R., Middleton, D., Boden, M., & Kobe, B. (2015). A bioinformatics tool for epitope-based vaccine design that accounts for human ethnic diversity: Application to emerging infectious diseases. Vaccine, 33(10), 1267–1273. https://doi.org/10.1016/j.vaccine.2015.01.040
   PubMed Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Polymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52(12), 7182–7190. https://doi.org/10.1063/1.328693
   Web of Science ®Google Scholar
• Pereira, J., Simpkin, A. J., Hartmann, M. D., Rigden, D. J., Keegan, R. M., & Lupas, A. N. (2021). High-accuracy protein structure prediction in CASP14. Proteins, 89(12), 1687–1699. https://doi.org/10.1002/prot.26171
   PubMed Web of Science ®Google Scholar
• Reynisson, B., Alvarez, B., Paul, S., Peters, B., & Nielsen, M. (2020). NetMHCpan-4.1 and NetMHCIIpan-4.0: Improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data. Nucleic Acids Research, 48(W1), W449–W454. https://doi.org/10.1093/nar/gkaa379
   PubMed Web of Science ®Google Scholar
• Ribeiro, J. MAzevedo,., & J. A., R. (1961). La peste porcine Africaine au Portugal. Bulletin - Office International des épizooties, 55, 88–106.
   Google Scholar
• Ros-Lucas, A., Correa-Fiz, F., Bosch-Camós, L., Rodriguez, F., & Alonso-Padilla, J. (2020). Computational analysis of African Swine Fever Virus protein space for the design of an epitope-based vaccine ensemble. Pathogens, 9(12), 1078. https://doi.org/10.3390/pathogens9121078
   PubMed Web of Science ®Google Scholar
• Sanchez-Trincado, J. L., Gomez-Perosanz, M., & Reche, P. A. (2017). Fundamentals and methods for T- and B-cell epitope prediction. Journal of Immunology Research, 2017, 1–14. https://doi.org/10.1155/2017/2680160
   Web of Science ®Google Scholar
• Sánchez-Vizcaíno, J. M., Mur, L., & Martínez-López, B. (2012). African Swine Fever: An epidemiological update. Transboundary and Emerging Diseases, 59, 27–35. https://doi.org/10.1111/j.1865-1682.2011.01293.x
   PubMed Web of Science ®Google Scholar
• Sbai, H., Mehta, A., & DeGroot, A. (2001). Use of T cell epitopes for vaccine development. Current Drug Targets. Infectious Disorders, 1(3), 303–313. https://doi.org/10.2174/1568005014605955
   PubMedGoogle Scholar
• Schlake, T., Thess, A., Fotin-Mleczek, M., & Kallen, K.-J. (2012). Developing mRNA-vaccine technologies. RNA Biology, 9(11), 1319–1330. https://doi.org/10.4161/rna.22269
   PubMed Web of Science ®Google Scholar
• Sette, A., & Fikes, J. (2003). Epitope-based vaccines: An update on epitope identification, vaccine design and delivery. Current Opinion in Immunology, 15(4), 461–470. https://doi.org/10.1016/s0952-7915(03)00083-9
   PubMed Web of Science ®Google Scholar
• States, F. A. A. O. O. T. U. (2022). African Swine Fever (ASF), https://www.fao.org/ag/againfo/programmes/en/empres/ASF/index.html
   Google Scholar
• Suhrbier, A. (1997). Multi-epitope DNA vaccines. Immunology and Cell Biology, 75(4), 402–408. https://doi.org/10.1038/icb.1997.63
   PubMed Web of Science ®Google Scholar
• Supervision, T. F. S. f. V. a. P. (2022). The Federal Service for Veterinary and Phytosanitary Supervision, http://www.fsvps.ru.
   Google Scholar
• System, W. A. H. I. (2022). OIE-WAHIS - Outbreaks from the most recent events, https://wahis.oie.int/#/home.
   Google Scholar
• Tulman, E. R., Delhon, G. A., Ku, B. K., & Rock, D. L. (2009). Lesser known large dsDNA viruses (pp. 43–87). Springer.
   Google Scholar
• van Zundert, G. C. P., Rodrigues, J. P. G. L. M., Trellet, M., Schmitz, C., Kastritis, P. L., Karaca, E., Melquiond, A. S. J., van Dijk, M., de Vries, S. J., & Bonvin, A. M. J. J. (2016). The HADDOCK2.2 Web Server: User-friendly integrative modeling of biomolecular complexes. Journal of Molecular Biology, 428(4), 720–725. https://doi.org/10.1016/j.jmb.2015.09.014
   PubMed Web of Science ®Google Scholar
• Vangone, A., Spinelli, R., Scarano, V., Cavallo, L., & Oliva, R. (2011). COCOMAPS: A web application to analyze and visualize contacts at the interface of biomolecular complexes. Bioinformatics (Oxford, England), 27(20), 2915–2916. https://doi.org/10.1093/bioinformatics/btr484
   PubMed Web of Science ®Google Scholar
• Wang, W.-H., Lin, C.-Y., Chang Ishcol, M. R., Urbina, A. N., Assavalapsakul, W., Thitithanyanont, A., Lu, P.-L., Chen, Y.-H., & Wang, S.-F. (2019). Detection of African swine fever virus in pork products brought to Taiwan by travellers. Emerging Microbes & Infections, 8(1), 1000–1002. https://doi.org/10.1080/22221751.2019.1636615
   PubMed Web of Science ®Google Scholar
• Yonekura, K., Maki-Yonekura, S., & Namba, K. (2003). Complete atomic model of the bacterial flagellar filament by electron cryomicroscopy. Nature, 424(6949), 643–650. https://doi.org/10.1038/nature01830
   PubMed Web of Science ®Google Scholar
• Yoo, D., Kim, H., Lee, J. Y., & Yoo, H. S. (2020). African swine fever: Etiology, epidemiological status in Korea, and perspective on control. Journal of Veterinary Science, 21(2), e38. https://doi.org/10.4142/jvs.2020.21.e38
   PubMed Web of Science ®Google Scholar
• Zhang, J., & Tao, A. (2015). Allergy bioinformatics (pp. 175–186). Springer.
   Google Scholar
• Zsak, L., Onisk, D. V., Afonso, C. L., & Rock, D. L. (1993). Virulent African Swine Fever virus isolates are neutralized by swine immune serum and by monoclonal antibodies recognizing a 72-kDa viral protein. Virology, 196(2), 596–602. https://doi.org/10.1006/viro.1993.1515
   PubMed Web of Science ®Google Scholar