Mining of Ebola virus genome for the construction of multi-epitope vaccine to combat its infection

References

• Ajisegiri, W. S., Chughtai, A. A., & MacIntyre, C. R. (2018). A risk analysis approach to prioritizing epidemics: Ebola virus disease in West Africa as a case study. Risk Analysis, 38(3), 429–441. https://doi.org/https://doi.org/10.1111/risa.12876
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J., Postma, J. v., van Gunsteren, W. F., DiNola, A., & Haak, J. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Biedenkopf, N., Hartlieb, B., Hoenen, T., & Becker, S. (2013). Phosphorylation of Ebola virus VP30 influences the composition of the viral nucleocapsid complex: Impact on viral transcription and replication. The Journal of Biological Chemistry, 288(16), 11165–11174. https://doi.org/https://doi.org/10.1074/jbc.M113.461285
   PubMed Web of Science ®Google Scholar
• Bounds, C. E., Terry, F. E., Moise, L., Hannaman, D., Martin, W. D., De Groot, A. S., Suschak, J. J., Dupuy, L. C., & Schmaljohn, C. S. (2017). An immunoinformatics-derived DNA vaccine encoding human class II T cell epitopes of Ebola virus, Sudan virus, and Venezuelan equine encephalitis virus is immunogenic in HLA transgenic mice. Human Vaccines & Immunotherapeutics, 13(12), 2824–2836. https://doi.org/https://doi.org/10.1080/21645515.2017.1329788
   PubMedGoogle Scholar
• Broadfield, E., McKeever, T. M., Scrivener, S., Venn, A., Lewis, S. A., & Britton, J. (2002). Increase in the prevalence of allergen skin sensitization in successive birth cohorts. The Journal of Allergy and Clinical Immunology, 109(6), 969–974. https://doi.org/https://doi.org/10.1067/mai.2002.124772
   PubMed Web of Science ®Google Scholar
• Bui, H. H., Sidney, J., Dinh, K., Southwood, S., Newman, M. J., & Sette, A. (2006). Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics, 7, 153. https://doi.org/https://doi.org/10.1186/1471-2105-7-153
   PubMed Web of Science ®Google Scholar
• Bukreyev, A. A., Chandran, K., Dolnik, O., Dye, J. M., Ebihara, H., Leroy, E. M., Mühlberger, E., Netesov, S. V., Patterson, J. L., Paweska, J. T., Saphire, E. O., Smither, S. J., Takada, A., Towner, J. S., Volchkov, V. E., Warren, T. K., & Kuhn, J. H. (2014). Discussions and decisions of the 2012–2014 International Committee on Taxonomy of Viruses (ICTV) Filoviridae Study Group, January 2012–June 2013. Archives of Virology, 159(4), 821–830. https://doi.org/https://doi.org/10.1007/s00705-013-1846-9
   PubMed Web of Science ®Google Scholar
• Calis, J. J. A., Maybeno, M., Greenbaum, J. A., Weiskopf, D., De Silva, A. D., Sette, A., Keşmir, C., & Peters, B. (2013). Properties of MHC Class I presented peptides that enhance immunogenicity. PLoS Computational Biology, 9(10), e1003266. https://doi.org/https://doi.org/10.1371/journal.pcbi.1003266
   PubMed Web of Science ®Google Scholar
• Case, D. A., Ben-Shalom, I. Y., Brozell, S. R., Cerutti, D. S., Cheatham, I. T. E., Cruzeiro, V. W. D., Darden, T. A., Duke, R. E., Ghoreishi, D., Gilson, M. K., Gohlke, H., Goetz, A. W., Greene, D., Harris, R., Homeyer, N., Huang, Y., Izadi, S., Kovalenko, A., Kurtzman, T., … Kollman, D. M. Y. a. P. A. (2018). AMBER 2018. University of California, San Francisco.
   Google Scholar
• Cenciarelli, O., Gabbarini, V., Pietropaoli, S., Malizia, A., Tamburrini, A., Ludovici, G. M., Carestia, M., Giovanni, D. D., Sassolini, A., Palombi, L., Bellecci, C., & Gaudio, P. (2015). Viral bioterrorism: Learning the lesson of Ebola virus in West Africa 2013–2015. Virus Research, 210, 318–326. https://doi.org/https://doi.org/10.1016/j.virusres.2015.09.002
   PubMed Web of Science ®Google Scholar
• Cheng, J., Randall, A. Z., Sweredoski, M. J., & Baldi, P. (2005). SCRATCH: A protein structure and structural feature prediction server. Nucleic Acids Res, 33(Web Server issue), W72–6. https://doi.org/https://doi.org/10.1093/nar/gki396
   PubMedGoogle Scholar
• Coller, B. G., Blue, J., Das, R., Dubey, S., Finelli, L., Gupta, S., Helmond, F., Grant-Klein, R. J., Liu, K., Simon, J., Troth, S., VanRheenen, S., Waterbury, J., Wivel, A., Wolf, J., Heppner, D. G., Kemp, T., Nichols, R., & Monath, T. P. (2017). Clinical development of a recombinant Ebola vaccine in the midst of an unprecedented epidemic. Vaccine, 35(35 Pt A), 4465–4469. https://doi.org/https://doi.org/10.1016/j.vaccine.2017.05.097
   PubMed Web of Science ®Google Scholar
• Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log (N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Dash, R., Das, R., Junaid, M., Akash, M. F. C., Islam, A., & Hosen, S. Z. (2017). In silico-based vaccine design against Ebola virus glycoprotein. Advances and Applications in Bioinformatics and Chemistry, 10, 11–28. https://doi.org/https://doi.org/10.2147/AABC.S115859
   Google Scholar
• Dhanda, S. K., Vir, P., & Raghava, G. P. (2013). Designing of interferon-gamma inducing MHC class-II binders. Biology Direct, 8(1), 30. https://doi.org/https://doi.org/10.1186/1745-6150-8-30
   PubMed Web of Science ®Google Scholar
• Dimitrov, I., Flower, D. R., & Doytchinova, I. (2013). AllerTOP-a server for in silico prediction of allergens. BMC Bioinformatics, 14(Suppl 6), S4. https://doi.org/https://doi.org/10.1186/1471-2105-14-S6-S4
   PubMed 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/https://doi.org/10.1093/bioinformatics/btt619
   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/https://doi.org/10.1186/1471-2105-8-4
   PubMed Web of Science ®Google Scholar
• El-Manzalawy, Y., Dobbs, D., & Honavar, V. (2008). Predicting linear B-cell epitopes using string kernels. Journal of Molecular Recognition, 21(4), 243–255. https://doi.org/https://doi.org/10.1002/jmr.893
   PubMed Web of Science ®Google Scholar
• Feldmann, H., Muhlberger, E., Randolf, A., Will, C., Kiley, M. P., Sanchez, A., & Klenk, H. D. (1992). Marburg virus, a filovirus: Messenger RNAs, gene order, and regulatory elements of the replication cycle. Virus Research, 24(1), 1–19. https://doi.org/https://doi.org/10.1016/0168-1702(92)90027-7
   PubMed Web of Science ®Google Scholar
• Fraser, C. C., Altreuter, D. H., Ilyinskii, P., Pittet, L., LaMothe, R. A., Keegan, M., Johnston, L., & Kishimoto, T. K. (2014). Generation of a universal CD4 memory T cell recall peptide effective in humans, mice and non-human primates. Vaccine, 32(24), 2896–2903. https://doi.org/https://doi.org/10.1016/j.vaccine.2014.02.024
   PubMed Web of Science ®Google Scholar
• Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D., & Bairoch, A. (2003). ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Research, 31(13), 3784–3788. https://doi.org/https://doi.org/10.1093/nar/gkg563
   PubMed Web of Science ®Google Scholar
• Gohlke, H., & Case, D. A. (2004). Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. Journal of Computational Chemistry, 25(2), 238–250. https://doi.org/https://doi.org/10.1002/jcc.10379
   PubMed Web of Science ®Google Scholar
• Gohlke, H., Kiel, C., & Case, D. A. (2003). Insights into protein–protein binding by binding free energy calculation and free energy decomposition for the Ras–Raf and Ras–RalGDS complexes. Journal of Molecular Biology, 330(4), 891–913. https://doi.org/https://doi.org/10.1016/S0022-2836(03)00610-7
   PubMed Web of Science ®Google Scholar
• Gross, L., Lhomme, E., Pasin, C., Richert, L., & Thiebaut, R. (2018). Ebola vaccine development: Systematic review of pre-clinical and clinical studies, and meta-analysis of determinants of antibody response variability after vaccination. International Journal of Infectious Diseases, 74, 83–96. https://doi.org/https://doi.org/10.1016/j.ijid.2018.06.022
   PubMed Web of Science ®Google Scholar
• Harty, R. N., Brown, M. E., Wang, G., Huibregtse, J., & Hayes, F. P. (2000). A PPxY motif within the VP40 protein of Ebola virus interacts physically and functionally with a ubiquitin ligase: Implications for filovirus budding. Proceedings of the National Academy of Sciences of the United States of America, 97(25), 13871–13876. https://doi.org/https://doi.org/10.1073/pnas.250277297
   PubMed Web of Science ®Google Scholar
• Hedayat, M., Netea, M. G., & Rezaei, N. (2011). Targeting of Toll-like receptors: A decade of progress in combating infectious diseases. The Lancet, 11(9), 702–712. https://doi.org/https://doi.org/10.1016/S1473-3099(11)70099-8
   Web of Science ®Google Scholar
• Heo, L., Park, H., & Seok, C. (2013). GalaxyRefine: Protein structure refinement driven by side-chain repacking. Nucleic Acids Research, 41(Web Server issue), W384–388. https://doi.org/https://doi.org/10.1093/nar/gkt458
   PubMed Web of Science ®Google Scholar
• Homeyer, N., & Gohlke, H. (2012). Free energy calculations by the molecular mechanics Poisson-Boltzmann Surface Area Method. Molecular Informatics, 31(2), 114–122. https://doi.org/https://doi.org/10.1002/minf.201100135
   PubMed Web of Science ®Google Scholar
• Hubbard, R. E., & Haider, M. K. (2010). Hydrogen bonds in proteins: Role and strength. eLS.
   Google Scholar
• Jonniya, N. A., Sk, M. F., & Kar, P. (2019). Investigating phosphorylation-induced conformational changes in WNK1 kinase by molecular dynamics simulations. ACS Omega, 4(17), 17404–17416. https://doi.org/https://doi.org/10.1021/acsomega.9b02187
   PubMed Web of Science ®Google Scholar
• Jonniya, N. A., Sk, M. F., & Kar, P. (2020). A comparative study of structural and conformational properties of WNK kinase isoforms bound to an inhibitor: Insights from molecular dynamic simulations. Journal of Biomolecular Structure and Dynamics, 1-16. https://doi.org/https://doi.org/10.1080/07391102.07392020.01827035.
   Google Scholar
• Jung, I. D., Jeong, S. K., Lee, C. M., Noh, K. T., Heo, D. R., Shin, Y. K., Yun, C. H., Koh, W. J., Akira, S., Whang, J., Kim, H. J., Park, W. S., Shin, S. J., & Park, Y. M. (2011). Enhanced efficacy of therapeutic cancer vaccines produced by co-treatment with Mycobacterium tuberculosis heparin-binding hemagglutinin, a novel TLR4 agonist. Cancer Research, 71(8), 2858–2870. https://doi.org/https://doi.org/10.1158/0008-5472.CAN-10-3487
   PubMed Web of Science ®Google Scholar
• Kalita, P., Padhi, A. K., Zhang, K. Y. J., & Tripathi, T. (2020). Design of a peptide-based subunit vaccine against novel coronavirus SARS-CoV-2. Microbial Pathogenesis, 145, 104236. https://doi.org/https://doi.org/10.1016/j.micpath.2020.104236
   PubMed Web of Science ®Google Scholar
• Kar, P., & Knecht, V. (2012a). Energetics of mutation-induced changes in potency of lersivirine against HIV-1 reverse transcriptase. Journal of Physical Chemistry B, 116(22), 6269–6278. https://doi.org/https://doi.org/10.1021/jp300818c
   PubMed Web of Science ®Google Scholar
• Kar, P., & Knecht, V. (2012b). Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir. Journal of Computer-Aided Molecular Design, 26(2), 215–232. https://doi.org/https://doi.org/10.1007/s10822-012-9550-5
   PubMed Web of Science ®Google Scholar
• Kar, P., & Knecht, V. (2012c). Origin of decrease in potency of darunavir and two related antiviral inhibitors against HIV-2 compared to HIV-1 protease. The Journal of Physical Chemistry B, 116(8), 2605–2614. https://doi.org/https://doi.org/10.1021/jp211768n
   PubMed Web of Science ®Google Scholar
• Kar, P., & Knecht, V. (2012d). Mutation-induced loop opening and energetics for binding of tamiflu to influenza N8 neuraminidase. The Journal of Physical Chemistry B, 116(21), 6137–6149. https://doi.org/https://doi.org/10.1021/jp3022612
   PubMed Web of Science ®Google Scholar
• Khan, M. A., Hossain, M. U., Rakib-Uz-Zaman, S. M., & Morshed, M. N. (2015). Epitope-based peptide vaccine design and target site depiction against Ebola viruses: An immunoinformatics study. Scandinavian Journal of Immunology, 82(1), 25–34. https://doi.org/https://doi.org/10.1111/sji.12302
   PubMed Web of Science ®Google Scholar
• Kollman, P. A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M., Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case, D. A., & Cheatham, T. E. (2000). Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models. Accounts of Chemical Research, 33(12), 889–897. https://doi.org/https://doi.org/10.1021/ar000033j
   PubMed Web of Science ®Google Scholar
• Kozakov, D., Hall, D. R., Xia, B., Porter, K. A., Padhorny, D., Yueh, C., Beglov, D., & Vajda, S. (2017). The ClusPro web server for protein-protein docking. Nature Protocols, 12(2), 255–278. https://doi.org/https://doi.org/10.1038/nprot.2016.169
   PubMed Web of Science ®Google Scholar
• Kräutler, V., van Gunsteren, W. F., & Hünenberger, P. H. (2001). A fast SHAKE algorithm to solve distance constraint equations for small molecules in molecular dynamics simulations. Journal of Computational Chemistry, 22(5), 501–508. https://doi.org/https://doi.org/10.1002/1096-987X(20010415)22:5<501::AID-JCC1021>3.0.CO;2-V
   Web of Science ®Google Scholar
• Larsen, M. V., Lundegaard, C., Lamberth, K., Buus, S., Lund, O., & Nielsen, M. (2007). Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction. BMC Bioinformatics, 8, 424. https://doi.org/https://doi.org/10.1186/1471-2105-8-424
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/https://doi.org/10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Lee, J., Nyenhuis, D. A., Nelson, E. A., Cafiso, D. S., White, J. M., & Tamm, L. K. (2017). Structure of the Ebola virus envelope protein MPER/TM domain and its interaction with the fusion loop explains their fusion activity. Proceedings of the National Academy of Sciences of the United States of America, 114(38), E7987–E7996. https://doi.org/https://doi.org/10.1073/pnas.1708052114
   PubMed Web of Science ®Google Scholar
• Liu, H., & Irvine, D. J. (2015). Guiding principles in the design of molecular bioconjugates for vaccine applications. Bioconjugate Chemistry, 26(5), 791–801. https://doi.org/https://doi.org/10.1021/acs.bioconjchem.5b00103
   PubMed Web of Science ®Google Scholar
• Lizbeth, R.-S. G., Jazmín, G.-M., José, C.-B., & Marlet, M.-A. (2020). Immunoinformatics study to search epitopes of spike glycoprotein from SARS-CoV-2 as potential vaccine. Journal of Biomolecular Structure and Dynamics, 1–15.
   PubMed Web of Science ®Google Scholar
• Lupton, H., Lambert, R., Bumgardner, D., Moe, J., & Eddy, G. (1980). Inactivated vaccine for Ebola virus efficacious in guineapig model. The Lancet, 316(8207), 1294–1295. https://doi.org/https://doi.org/10.1016/S0140-6736(80)92352-1
   Google Scholar
• Mahanty, S., & Bray, M. (2004). Pathogenesis of filoviral haemorrhagic fevers. The Lancet, 4(8), 487–498. https://doi.org/https://doi.org/10.1016/S1473-3099(04)01103-X
   Web of Science ®Google Scholar
• Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/https://doi.org/10.1021/acs.jctc.5b00255
   PubMed Web of Science ®Google Scholar
• Majee, P., Jain, N., & Kumar, A. (2020). Designing of a multi-epitope vaccine candidate against Nipah virus by in silico approach: A putative prophylactic solution for the deadly virus. Journal of Biomolecular Structure and Dynamics, 1–20.
   PubMed Web of Science ®Google Scholar
• Martinez, M. J., Volchkova, V. A., Raoul, H., Alazard-Dany, N., Reynard, O., & Volchkov, V. E. (2011). Role of VP30 phosphorylation in the Ebola virus replication cycle. The Journal of Infectious Diseases, 204(Suppl 3), S934–S940. https://doi.org/https://doi.org/10.1093/infdis/jir320
   PubMedGoogle Scholar
• McGuffin, L. J., Bryson, K., & Jones, D. T. (2000). The PSIPRED protein structure prediction server. Bioinformatics (Oxford, England), 16(4), 404–405. https://doi.org/https://doi.org/10.1093/bioinformatics/16.4.404
   PubMed Web of Science ®Google Scholar
• Miller, B. R., III, McGee, T. D., Jr., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. https://doi.org/https://doi.org/10.1021/ct300418h
   PubMed Web of Science ®Google Scholar
• Mora, M., Veggi, D., Santini, L., Pizza, M., & Rappuoli, R. (2003). Reverse vaccinology. Drug Discovery Today, 8(10), 459–464. https://doi.org/https://doi.org/10.1016/S1359-6446(03)02689-8
   PubMed Web of Science ®Google Scholar
• Moxon, R., Reche, P. A., & Rappuoli, R. (2019). Editorial: Reverse vaccinology. Frontiers in Immunology, 10, 2776. https://doi.org/https://doi.org/10.3389/fimmu.2019.02776
   PubMed Web of Science ®Google Scholar
• Ojha, R., Pareek, A., Pandey, R. K., Prusty, D., & Prajapati, V. K. (2019). Strategic development of a next-generation multi-epitope vaccine to prevent nipah virus zoonotic infection. ACS Omega, 4(8), 13069–13079. https://doi.org/https://doi.org/10.1021/acsomega.9b00944
   PubMed Web of Science ®Google Scholar
• Okumura, A., Pitha, P. M., Yoshimura, A., & Harty, R. N. (2010). Interaction between Ebola virus glycoprotein and host toll-like receptor 4 leads to induction of proinflammatory cytokines and SOCS1. Journal of Virology, 84(1), 27–33. https://doi.org/https://doi.org/10.1128/JVI.01462-09
   PubMed Web of Science ®Google Scholar
• Pastor, R. W., Brooks, B. R., & Szabo, A. (1988). An analysis of the accuracy of Langevin and molecular dynamics algorithms. Molecular Physics, 65(6), 1409–1419. https://doi.org/https://doi.org/10.1080/00268978800101881
   Web of Science ®Google Scholar
• Price, D. J., & Brooks, C. L. III (2004). A modified TIP3P water potential for simulation with Ewald summation. Journal of Chemical Physics, 121(20), 10096–10103. https://doi.org/https://doi.org/10.1063/1.1808117
   PubMed Web of Science ®Google Scholar
• Reed, S. G., Bertholet, S., Coler, R. N., & Friede, M. (2009). New horizons in adjuvants for vaccine development. Trends in Immunology, 30(1), 23–32. https://doi.org/https://doi.org/10.1016/j.it.2008.09.006
   PubMed Web of Science ®Google Scholar
• Roe, D. R., & Cheatham, T. E. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. https://doi.org/https://doi.org/10.1021/ct400341p
   PubMed Web of Science ®Google Scholar
• Saghazadeh, A., & Rezaei, N. (2017). Implications of Toll-like receptors in Ebola infection. Expert Opinion on Therapeutic Targets, 21(4), 415–425. https://doi.org/https://doi.org/10.1080/14728222.2017.1299128
   PubMed Web of Science ®Google Scholar
• Saha, S., & Raghava, G. P. S. (2006). AlgPred: Prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Research, 34(Web Server issue), W202–W209. https://doi.org/https://doi.org/10.1093/nar/gkl343
   PubMed Web of Science ®Google Scholar
• Samad, A., Ahammad, F., Nain, Z., Alam, R., Imon, R. R., Hasan, M., & Rahman, M. S. (2020). Designing a multi-epitope vaccine against SARS-CoV-2: An immunoinformatics approach. Journal of Biomolecular Structure and Dynamics, 1–17.
   PubMed Web of Science ®Google Scholar
• Sanchez, A., Kiley, M. P., Holloway, B. P., & Auperin, D. D. (1993). Sequence analysis of the Ebola virus genome: Organization, genetic elements, and comparison with the genome of Marburg virus. Virus Research, 29(3), 215–240. https://doi.org/https://doi.org/10.1016/0168-1702(93)90063-S
   PubMed Web of Science ®Google Scholar
• Sharma, R., Jangid, K., & Anuradha. (2017). Ebola vaccine: How far are we? Journal of Clinical and Diagnostic Research, 11(5), DE01–DE04. https://doi.org/https://doi.org/10.7860/JCDR/2017/22184.9863
   PubMed Web of Science ®Google Scholar
• Singh, S., Sk, M. F., Sonawane, A., Kar, P., & Sadhukhan, S. (2020). Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA‐dependent RNA polymerase (RdRp) inhibition: An in-silico analysis. Journal of Biomolecular Structure and Dynamics. https://doi.org/https://doi.org/10.1080/07391102.07392020.01796810
   Google Scholar
• Sk, M. F., Jonniya, N. A., & Kar, P. (2020a). Exploring the energetic basis of binding of currently used drugs against HIV-1 subtype CRF01_AE protease via molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics, 1–18. https://doi.org/https://doi.org/10.1080/07391102.07392020.01794965
   Google Scholar
• Sk, M. F., Jonniya, N. A., Roy, R., Poddar, S., & Kar, P. (2020b). Computational investigation of structural dynamics of SARS-CoV-2 methyltransferase-stimulatory factor heterodimer nsp16/nsp10 bound to the cofactor SAM. Frontiers in Molecular Biosciences, 7, 353. https://doi.org/https://doi.org/10.3389/fmolb.2020.590165
   Web of Science ®Google Scholar
• Sk, M. F., Roy, R., & Kar, P. (2020c). Exploring the potency of currently used drugs against HIV-1 protease of subtype D variant by using multiscale simulations. Journal of Biomolecular Structure and Dynamics, 1–16. https://doi.org/https://doi.org/10.1080/07391102.07392020.01724196
   Google Scholar
• Sk, M. F., Roy, R., Jonniya, N. A., Poddar, S., & Kar, P. (2020d). Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/https://doi.org/10.1080/07391102.07392020.01768149
   Google Scholar
• Sullivan, N. J., Sanchez, A., Rollin, P. E., Yang, Z. Y., & Nabel, G. J. (2000). Development of a preventive vaccine for Ebola virus infection in primates. Nature, 408(6812), 605–609. https://doi.org/https://doi.org/10.1038/35046108
   PubMed Web of Science ®Google Scholar
• To, K. K., Chan, J. F., Tsang, A. K., Cheng, V. C., & Yuen, K. Y. (2015). Ebola virus disease: A highly fatal infectious disease reemerging in West Africa. Microbes and Infection, 17(2), 84–97. https://doi.org/https://doi.org/10.1016/j.micinf.2014.11.007
   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/https://doi.org/10.1093/protein/8.2.127
   PubMedGoogle Scholar
• Wang, D., Raja, N. U., Trubey, C. M., Juompan, L. Y., Luo, M., Woraratanadharm, J., Deitz, S. B., Yu, H., Swain, B. M., Moore, K. M., Pratt, W. D., Hart, M. K., & Dong, J. Y. (2006). Development of a cAdVax-based bivalent Ebola virus vaccine that induces immune responses against both the Sudan and Zaire species of Ebola virus. Journal of Virology, 80(6), 2738–2746. https://doi.org/https://doi.org/10.1128/JVI.80.6.2738-2746.2006
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Yang, J., Yan, R., Roy, A., Xu, D., Poisson, J., & Zhang, Y. (2015). The I-TASSER Suite: Protein structure and function prediction. Nature Methods, 12(1), 7–8. https://doi.org/https://doi.org/10.1038/nmeth.3213
   PubMed Web of Science ®Google Scholar
• Zheng, Q., Li, Z., Zhou, S., Zhang, Q., Zhou, L., Fu, X., Yang, L., Ma, Y., & Hao, X. (2017). Heparin-binding hemagglutinin of Mycobacterium tuberculosis is an inhibitor of autophagy. Frontiers in Cellular and Infection Microbiology, 7, 33–33. https://doi.org/https://doi.org/10.3389/fcimb.2017.00033
   PubMed Web of Science ®Google Scholar