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/https://doi.org/10.1016/j.softx.2015.06.001
- Adhikari, U. K., Tayebi, M., & Rahman, M. M. (2018). Immunoinformatics approach for epitope-based peptide vaccine design and active site prediction against polyprotein of emerging oropouche virus. Journal of Immunology Research, 2018, 6718083. https://doi.org/https://doi.org/10.1155/2018/6718083
- 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(1), 9232. https://doi.org/https://doi.org/10.1038/s41598-017-09199-w
- Arai, R., Ueda, H., Kitayama, A., Kamiya, N., & Nagamune, T. (2001). Design of the linkers which effectively separate domains of a bifunctional fusion protein. Protein Engineering, 14(8), 529–532. https://doi.org/https://doi.org/10.1093/protein/14.8.529
- Azim, K. F., Hasan, M., Hossain, M. N., Somana, S. R., Hoque, S. F., Bappy, M., Chowdhury, A. T., & Lasker, T. (2019). Immunoinformatics approaches for designing a novel multi epitope peptide vaccine against human norovirus (Norwalk virus). Infection, Genetics and Evolution, 74, 103936. https://doi.org/https://doi.org/10.1016/j.meegid.2019.103936
- Ba, Y., Trouillet, J., Thonnon, J., & Fontenille, D. (1999). Phlébotomes du Sénégal: Inventaire de la faune de la région de Kédougou. Isolements d'arbovirus [Phlebotomus of Senegal: Survey of the fauna in the region of Kedougou. Isolation of arbovirus]. Bulletin de la Societe de Pathologie Exotique (1990), 92(2), 131–135.
- Banerjee, A. K. (1987). Transcription and replication of rhabdoviruses. Microbiological Reviews, 51(1), 66–87.
- Bhatt, P. N., & Rodrigues, F. M. (1967). Chandipura: A new Arbovirus isolated in India from patients with febrile illness. The Indian Journal of Medical Research, 55(12), 1295–1305.
- Bui, H. H., Sidney, J., Li, W., Fusseder, N., & Sette, A. (2007). Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics, 8, 361. https://doi.org/https://doi.org/10.1186/1471-2105-8-361
- 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, 842329. https://doi.org/https://doi.org/10.1155/2012/842329
- Dedhia, L., Gadekar, S., Mehta, P., & Parekh, S. (2015). HLA haplotype diversity in the South Indian population and its relevance. Indian Journal of Transplantation, 9(4), 138–143. https://doi.org/https://doi.org/10.1016/j.ijt.2015.10.016
- Dhanda, S. K., Gupta, S., Vir, P., & Raghava, G. P. (2013). Prediction of IL4 inducing peptides. Clinical and Developmental Immunology, 2013, 263952. https://doi.org/https://doi.org/10.1155/2013/263952
- Dietzschold, B., Wang, H. H., Rupprecht, C. E., Celis, E., Tollis, M., Ertl, H., Heber-Katz, E., & Koprowski, H. (1987). Induction of protective immunity against rabies by immunization with rabies virus ribonucleoprotein. Proceedings of the National Academy of Sciences of the United States of America, 84(24), 9165–9169. https://doi.org/https://doi.org/10.1073/pnas.84.24.9165
- 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/https://doi.org/10.1186/1471-2105-8-4
- Fontenille, D., Traore-Lamizana, M., Trouillet, J., Leclerc, A., Mondo, M., Ba, Y., Digoutte, J. P., & Zeller, H. G. (1994). First isolations of arboviruses from phlebotomine sand flies in West Africa. The American Journal of Tropical Medicine and Hygiene, 50(5), 570–574. https://doi.org/https://doi.org/10.4269/ajtmh.1994.50.570
- 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/https://doi.org/10.1093/nar/gki376
- Gu, Y., Sun, X., Li, B., Huang, J., Zhan, B., & Zhu, X. (2017). Vaccination with a paramyosin-based multi-epitope vaccine elicits significant protective immunity against Trichinella spiralis infection in mice. Frontiers in Microbiology, 8, 1475. https://doi.org/https://doi.org/10.3389/fmicb.2017.01475
- Jadi, R. S., Sudeep, A. B., Barde, P. V., Arankalle, V. A., & Mishra, A. C. (2011). Development of an inactivated candidate vaccine against Chandipura virus (Rhabdoviridae: Vesiculovirus). Vaccine, 29(28), 4613–4617. https://doi.org/https://doi.org/10.1016/j.vaccine.2011.04.063
- 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/https://doi.org/10.1093/nar/gkx346
- Kaminski, G. A., Friesner, R. A., Tirado-Rives, J., & Jorgensen, W. L. (2001). Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. The Journal of Physical Chemistry B, 105(28), 6474–6487. https://doi.org/https://doi.org/10.1021/jp003919d
- Kemp, G. E. (1975). Viruses other than arenaviruses from West African wild mammals. Factors affecting transmission to man and domestic animals. Bulletin of the World Health Organization, 52(4–6), 615–620.
- Kolaskar, A. S., & Tongaonkar, P. C. (1990). A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Letters, 276(1–2), 172–174. https://doi.org/https://doi.org/10.1016/0014-5793(90)80535-Q
- Lovell, S. C., Davis, I. W., Arendall, W. B., de Bakker, P. I. W., Word, J. M., Prisant, M. G., Richardson, J. S., & Richardson, D. C. (2003). Structure validation by Calpha geometry: Phi,psi and Cbeta deviation. Proteins: Structure, Function, and Bioinformatics, 50(3), 437–450. https://doi.org/https://doi.org/10.1002/prot.10286
- Lund, J. M., Alexopoulou, L., Sato, A., Karow, M., Adams, N. C., Gale, N. W., Iwasaki, A., & Flavell, R. A. (2004). Recognition of single-stranded RNA viruses by Toll-like receptor 7. Proceedings of the National Academy of Sciences of the United States of America, 101(15), 5598–5603. https://doi.org/https://doi.org/10.1073/pnas.0400937101
- Mashiach, E., Schneidman-Duhovny, D., Andrusier, N., Nussinov, R., & Wolfson, H. J. (2008). FireDock: A web server for fast interaction refinement in molecular docking. Nucleic Acids Research, 36(Web Server issue), W229–W232. https://doi.org/https://doi.org/10.1093/nar/gkn186
- 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 T(CD8+)-cell responses to vaccinia virus. Nature Biotechnology, 24(7), 817–819. https://doi.org/https://doi.org/10.1038/nbt1215
- Nandy, A., & Basak, S. C. (2016). A brief review of computer-assisted approaches to rational design of peptide vaccines. International Journal of Molecular Sciences, 17(5), 666. https://doi.org/https://doi.org/10.3390/ijms17050666
- Narula, A., Pandey, R. K., Khatoon, N., Mishra, A., & Prajapati, V. K. (2018). Excavating chikungunya genome to design B and T cell multi-epitope subunit vaccine using comprehensive immunoinformatics approach to control chikungunya infection. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 61, 4–15. https://doi.org/https://doi.org/10.1016/j.meegid.2018.03.007
- Pavitrakar, D. V., Damle, R. G., Tripathy, A. S., & Shil, P. (2018). Identification of a conserved neutralizing epitope in the G-protein of Chandipura virus. Archives of Virology, 163(12), 3215–3223. https://doi.org/https://doi.org/10.1007/s00705-018-3987-3
- Peiris, J. S., Dittus, W. P., & Ratnayake, C. B. (1993). Seroepidemiology of dengue and other arboviruses in a natural population of toque macaques (Macaca sinica) at Polonnaruwa, Sri Lanka. Journal of Medical Primatology, 22(4), 240–245.
- Peng, J., & Xu, J. (2011). RaptorX: Exploiting structure information for protein alignment by statistical inference. Proteins, 79(Suppl 10), 161–171. https://doi.org/https://doi.org/10.1002/prot.23175
- Rao, B. L., Basu, A., Wairagkar, N. S., Gore, M. M., Arankalle, V. A., Thakare, J. P., Jadi, R. S., Rao, K. A., & Mishra, A. C. (2004). A large outbreak of acute encephalitis with high fatality rate in children in Andhra Pradesh, India, in 2003, associated with Chandipura virus. The Lancet, 364(9437), 869–874. https://doi.org/https://doi.org/10.1016/S0140-6736(04)16982-1
- 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/https://doi.org/10.1371/journal.pone.0009862
- Realegeno, S., Niezgoda, M., Yager, P. A., Kumar, A., Hoque, L., Orciari, L., Sambhara, S., Olson, V. A., & Satheshkumar, P. S. (2018). An ELISA-based method for detection of rabies virus nucleoprotein-specific antibodies in human antemortem samples. PloS One, 13(11), e0207009. https://doi.org/https://doi.org/10.1371/journal.pone.0207009
- Salvador, E. A., Pires de Souza, G. A., Cotta Malaquias, L. C., Wang, T., & Leomil Coelho, L. F. (2019). Identification of relevant regions on structural and nonstructural proteins of Zika virus for vaccine and diagnostic test development: An in silico approach. New Microbes and New Infections, 29, 100506. https://doi.org/https://doi.org/10.1016/j.nmni.2019.01.002
- Schneidman-Duhovny, D., Inbar, Y., Nussinov, R., & Wolfson, H. J. (2005). PatchDock and SymmDock: Servers for rigid and symmetric docking. Nucleic Acids Research, 33(Web Server issue), W363–W367. https://doi.org/https://doi.org/10.1093/nar/gki481
- Sharp, P. M., & Li, W. H. (1987). The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Research, 15(3), 1281–1295. https://doi.org/https://doi.org/10.1093/nar/15.3.1281
- Shukla, R., Shukla, H., Kalita, P., Sonkar, A., Pandey, T., Singh, D. B., Kumar, A., & Tripathi, T. (2018). Identification of potential inhibitors of Fasciola gigantica thioredoxin1: Computational screening, molecular dynamics simulation, and binding free energy studies. Journal of Biomolecular Structure & Dynamics, 36(8), 2147–2162. https://doi.org/https://doi.org/10.1080/07391102.2017.1344141
- Singh, A., Sharma, P., Kar, H. K., Sharma, V. K., Tembhre, M. K., Gupta, S., Laddha, N. C., Dwivedi, M., Begum, R., Gokhale, R. S., & Rani, R. (2012). HLA alleles and amino-acid signatures of the peptide-binding pockets of HLA molecules in vitiligo. The Journal of Investigative Dermatology, 132(1), 124–134. https://doi.org/https://doi.org/10.1038/jid.2011.240
- Skwarczynski, M., & Toth, I. (2014). Recent advances in peptide-based subunit nanovaccines. Nanomedicine (London, England), 9(17), 2657–2669. https://doi.org/https://doi.org/10.2217/nnm.14.187
- Sudeep, A. B., Gurav, Y. K., & Bondre, V. P. (2016). Changing clinical scenario in Chandipura virus infection. The Indian Journal of Medical Research, 143(6), 712–721. https://doi.org/https://doi.org/10.4103/0971-5916.191929
- Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013). MEGA6: Molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution, 30(12), 2725–2729. https://doi.org/https://doi.org/10.1093/molbev/mst197
- Tesh, R. B., & Modi, G. B. (1983). Growth and transovarial transmission of Chandipura virus (Rhabdoviridae: Vesiculovirus) in phlebotomus papatasi. The American Journal of Tropical Medicine and Hygiene, 32(3), 621–623. https://doi.org/https://doi.org/10.4269/ajtmh.1983.32.621
- Tripathy, A., Balaji, S., Rao, N., Thakare, J., Mishra, A., & Arankalle, V. (2005). Cytokine levels in Chandipura virus associated encephalopathy in children. Scandinavian Journal of Infectious Diseases, 37(8), 590–593. https://doi.org/https://doi.org/10.1080/00365540510044067
- Venkateswarlu, C. H., & Arankalle, V. A. (2010). Evaluation of the immunogenicity of a recombinant glycoprotein-based Chandipura vaccine in combination with commercially available DPT vaccine. Vaccine, 28(6), 1463–1467. https://doi.org/https://doi.org/10.1016/j.vaccine.2009.11.072
- Wang, P., Sidney, J., Dow, C., Mothé, B., Sette, A., & Peters, B. (2008). A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Computational Biology, 4(4), e1000048. https://doi.org/https://doi.org/10.1371/journal.pcbi.1000048
- Xu, D., & Zhang, Y. (2011). Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. Biophysical Journal, 101(10), 2525–2534. https://doi.org/https://doi.org/10.1016/j.bpj.2011.10.024
- Xue, L. C., Rodrigues, J. P., Kastritis, P. L., Bonvin, A. M., & Vangone, A. (2016). PRODIGY: A web server for predicting the binding affinity of protein-protein complexes. Bioinformatics (Oxford, England), 32(23), 3676–3678. https://doi.org/https://doi.org/10.1093/bioinformatics/btw514