Computational designing of a novel subunit vaccine for human cytomegalovirus by employing the immunoinformatics framework

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
• Akhtar, N., Joshi, A., Kaushik, V., Kumar, M., & Mannan, M. A.-U. (2021). 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
• Almofti, Y. A., Abd-Elrahman, K. A., Gassmallah, S. A. E., & Salih, M. A. (2018). Multi epitopes vaccine prediction against severe acute respiratory syndrome (SARS) coronavirus using immunoinformatics approaches. American Journal of Microbiological Research, 6(3), 94–114.
   Google Scholar
• Anderholm, K. M., Bierle, C. J., & Schleiss, M. R. (2016). Cytomegalovirus vaccines: Current status and future prospects. Drugs, 76(17), 1625–1645. https://doi.org/10.1007/s40265-016-0653-5
   PubMed Web of Science ®Google Scholar
• Andrusier, N., Nussinov, R., & Wolfson, H. J. (2007). FireDock: Fast interaction refinement in molecular docking. Proteins, 69(1), 139–159. https://doi.org/10.1002/prot.21495
   PubMed Web of Science ®Google Scholar
• 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/10.1093/protein/14.8.529
   PubMedGoogle Scholar
• Arvin, A., Campadelli-Fiume, G., Mocarski, E., Moore, P. S., Roizman, B., Whitley, R., & Yamanishi, K. (Eds.). (2007). Human herpesviruses: Biology, therapy, and immunoprophylaxis. Cambridge University Press.
   Google Scholar
• Bacchetta, R., Gregori, S., & Roncarolo, M. G. (2005). CD4+ regulatory T cells: Mechanisms of induction and effector function. Autoimmunity Reviews, 4(8), 491–496. https://doi.org/10.1016/j.autrev.2005.04.005
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. Journal of Chemical Physics., 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Biovia, D. S., Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., & Richmond, T. J. (2000). Dassault Systèmes BIOVIA, Discovery Studio Visualizer, v. 17.2, San Diego: Dassault Systèmes, 2016. Journal of Chemical Physics, 10, 0021–9991.
   Google Scholar
• Biswal, J. K., Bisht, P., Mohapatra, J. K., Ranjan, R., Sanyal, A., & Pattnaik, B. (2015). Application of a recombinant capsid polyprotein (P1) expressed in a prokaryotic system to detect antibodies against foot-and-mouth disease virus serotype O. Journal of Virological Methods, 215–216, 45–51. https://doi.org/10.1016/j.jviromet.2015.02.008
   PubMed Web of Science ®Google Scholar
• Buchan, D. W. A., & Jones, D. T. (2019). The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic Acids Research, 47(W1), W402–W407. https://doi.org/10.1093/nar/gkz297
   PubMed Web of Science ®Google Scholar
• Cano, R. L. E., & Lopera, H. D. E. (2013). Introduction to T and B lymphocytes. In J.-M. Anaya, Y. Shoenfeld, A. Rojas-Villarraga, R. A. Levy, & R. Cervera (Eds.), Autoimmunity: From bench to bedside [Internet]. El Rosario University Press.
   Google Scholar
• Carvalho, L. H., Sano, G-i., Hafalla, J. C., Morrot, A., De Lafaille, M. A. C., & Zavala, F. (2002). IL-4-secreting CD4+ T cells are crucial to the development of CD8+ T-cell responses against malaria liver stages. Nature Medicine, 8(2), 166–170. https://doi.org/10.1038/nm0202-166
   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, 842329. https://doi.org/10.1155/2012/842329
   PubMed Web of Science ®Google Scholar
• Chang, K. Y., & Yang, J. R. (2013). Analysis and prediction of highly effective antiviral peptides based on random forests. PLoS One, 8(8), e70166. https://doi.org/10.1371/journal.pone.0070166
   PubMed Web of Science ®Google Scholar
• Chaudhri, G., Quah, B. J., Wang, Y., Tan, A. H., Zhou, J., Karupiah, G., & Parish, C. R. (2009). T cell receptor sharing by cytotoxic T lymphocytes facilitates efficient virus control. Proceedings of the National Academy of Sciences of the United States of America, 106(35), 14984–14989. https://doi.org/10.1073/pnas.0906554106
   PubMed Web of Science ®Google Scholar
• Chong, L. C., & Khan, A. M. (2019). Vaccine target discovery. Encyclopedia of Bioinformatics and Computational Biology, 3, 241–251. https://doi.org/10.1016/B978-0-12-809633-8.20100-3
   Google Scholar
• Cooper, N. R., & Nemerow, G. R. (1984). The role of antibody and complement in the control of viral infections. Journal of Investigative Dermatology, 83(1 Suppl), 121s–127s. https://doi.org/10.1111/1523-1747.ep12281847
   PubMed Web of Science ®Google Scholar
• Craig, D. B., & Dombkowski, A. A. (2013). Disulfide by Design 2.0: A web-based tool for disulfide engineering in proteins. BMC Bioinformatics, 14, 346. https://doi.org/10.1186/1471-2105-14-346
   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. Journal of Chemical Physics., 98(12), 10089–10092. https://doi.org/10.1063/1.464397
   Web of Science ®Google Scholar
• Dhanda, S. K., Gupta, S., Vir, P., & Raghava, G. P. S. (2013a). Prediction of IL4 inducing peptides. Clinical and Developmental Immunology, 2013, 263952. https://doi.org/10.1155/2013/263952
   PubMedGoogle Scholar
• Dhanda, S. K., Vir, P., & Raghava, G. P. S. (2013b). Designing of interferon-gamma inducing MHC class-II binders. Biology Direct, 8, 30. 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/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/10.1093/bioinformatics/btt619
   PubMed Web of Science ®Google Scholar
• Dobbie, A. M. (2017). Evaluation and management of cytomegalovirus-associated congenital hearing loss. Current Opinion in Otolaryngology & Head and Neck Surgery, 25(5), 390–395. https://doi.org/10.1097/MOO.0000000000000401
   PubMed Web of Science ®Google Scholar
• Dolan, A., Cunningham, C., Hector, R. D., Hassan-Walker, A. F., Lee, L., Addison, C., Dargan, D. J., McGeoch, D. J., Gatherer, D., Emery, V. C., Griffiths, P. D., Sinzger, C., McSharry, B. P., Wilkinson, G. W. G., & Davison, A. J. (2004). Genetic content of wild-type human cytomegalovirus. The Journal of General Virology, 85(Pt 5), 1301–1312. https://doi.org/10.1099/vir.0.79888-0
   PubMedGoogle 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. The Open Vaccine Journal, 1(1), 4.
   Google Scholar
• Elamin Elhasan, L. M., Hassan, M. B., Elhassan, R. M., Abdelrhman, F. A., Salih, E. A., Ibrahim H, A., Mohamed, A. A., Osman, H. S., Khalil, M. S. M., Alsafi, A. A., Idris, A. B., & Hassan, M. A. (2021). Epitope-based peptide vaccine design against fructose bisphosphate aldolase of Candida glabrata: An immunoinformatics approach. Journal of Immunology Research, 2021, 8280925. https://doi.org/10.1155/2021/8280925
   PubMed Web of Science ®Google Scholar
• Elek, S. D., & Stern, H. (1974). Development of a vaccine against mental retardation caused by cytomegalovirus infection in utero. Lancet (London, England), 1(7845), 1–5. https://doi.org/10.1016/S0140-6736(74)92997-3
   PubMed Web of Science ®Google Scholar
• Feng, T., Chen, F., Kang, Y., Sun, H., Liu, H., Li, D., Zhu, F., & Hou, T. (2017). HawkRank: A new scoring function for protein-protein docking based on weighted energy terms. Journal of Cheminformatics, 9(1), 66. https://doi.org/10.1186/s13321-017-0254-7
   PubMed Web of Science ®Google Scholar
• Garcia, K. C., Teyton, L., & Wilson, I. A. (1999). Structural basis of T cell recognition. Annual Review of Immunology, 17, 369–397. https://doi.org/10.1146/annurev.immunol.17.1.369
   PubMed Web of Science ®Google Scholar
• Gasteiger, E., Hoogland, C., Gattiker, A., Wilkins, M. R., Appel, R. D., & Bairoch, A. (2005). Protein identification and analysis tools on the ExPASy server. In J. M. Walker (Ed.), The proteomics protocols handbook (pp. 571–607). Totowa,NJ: Springer. https://doi.org/10.1385/1-59259-890-0:571
   Google Scholar
• Grote, A., Hiller, K., Scheer, M., Munch, R., Nortemann, 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
• Gruber, A. R., Lorenz, R., Bernhart, S. H., Neubock, R., & Hofacker, I. L. (2008). The Vienna RNA websuite. Nucleic Acids Research, 36(Web Server issue), W70–W74. https://doi.org/10.1093/nar/gkn188
   PubMed Web of Science ®Google Scholar
• 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/10.3389/fmicb.2017.01475
   PubMed Web of Science ®Google Scholar
• Gupta, S., Kapoor, P., Chaudhary, K., Gautam, A., Kumar, R., Consortium, O. S. D. D., & Raghava, G. P. S. (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
• Guruprasad, K., Reddy, B. V., & Pandit, M. W. (1990). Correlation between stability of a protein and its dipeptide composition: A novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Engineering, 4(2), 155–161. https://doi.org/10.1093/protein/4.2.155
   PubMedGoogle Scholar
• Halary, F., Amara, A., Lortat-Jacob, H., Messerle, M., Delaunay, T., Houlès, C., Fieschi, F., Arenzana-Seisdedos, F., Moreau, J. F., & Déchanet-Merville, J. (2002). Human cytomegalovirus binding to DC-SIGN is required for dendritic cell infection and target cell trans-infection. Immunity, 17(5), 653–664. https://doi.org/10.1016/S1074-7613(02)00447-8
   PubMed Web of Science ®Google Scholar
• Hamasaki-Katagiri, N., Lin, B. C., Simon, J., Hunt, R. C., Schiller, T., Russek-Cohen, E., Komar, A. A., Bar, H., & Kimchi-Sarfaty, C. (2017). The importance of mRNA structure in determining the pathogenicity of synonymous and non-synonymous mutations in haemophilia. Haemophilia: The Official Journal of the World Federation of Hemophilia, 23(1), e8–e17. https://doi.org/10.1111/hae.13107
   PubMed Web of Science ®Google Scholar
• Hasan, M., Islam, S., Chakraborty, S., Mustafa, A. H., Azim, K. F., Joy, Z. F., Hossain, M. N., Foysal, S. H., & Hasan, M. N. (2020). Contriving a chimeric polyvalent vaccine to prevent infections caused by herpes simplex virus (type-1 and type-2): An exploratory immunoinformatic approach. Journal of Biomolecular Structure and Dynamics, 38(10), 2898–2915. https://doi.org/10.1080/07391102.2019.1647286
   PubMed Web of Science ®Google Scholar
• Hebditch, M., Carballo-Amador, M. A., Charonis, S., Curtis, R., & Warwicker, J. (2017). Protein-Sol: A web tool for predicting protein solubility from sequence. Bioinformatics (Oxford, England), 33(19), 3098–3100. https://doi.org/10.1093/bioinformatics/btx345
   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
• Hoque, M. N., Istiaq, A., Clement, R. A., Sultana, M., Crandall, K. A., Siddiki, A. Z., & Hossain, M. A. (2019). Metagenomic deep sequencing reveals association of microbiome signature with functional biases in bovine mastitis. Scientific Reports, 9(1), 13536. https://doi.org/10.1038/s41598-019-49468-4
   PubMedGoogle Scholar
• Hou, T., Wang, J., Li, Y., & Wang, W. (2011). Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. Journal of Chemical Information and Modeling, 51(1), 69–82. https://doi.org/10.1021/ci100275a
   PubMed Web of Science ®Google Scholar
• Ikai, A. (1980). Thermostability and aliphatic index of globular proteins. Journal of Biochemistry, 88(6), 1895–1898. https://doi.org/10.1093/oxfordjournals.jbchem.a133168
   PubMed Web of Science ®Google Scholar
• Jones, D. T. (1999). Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology, 292(2), 195–202. https://doi.org/10.1006/jmbi.1999.3091
   PubMed Web of Science ®Google Scholar
• Jurtz, V., Paul, S., Andreatta, M., Marcatili, P., Peters, B., & Nielsen, M. (2017). NetMHCpan-4.0: Improved peptide-MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data. Journal of Immunology (Baltimore, MD: 1950), 199(9), 3360–3368. https://doi.org/10.4049/jimmunol.1700893
   PubMed Web of Science ®Google Scholar
• Kagami, L. P., das Neves, G. M., Timmers, L. F. S. M., Caceres, R. A., & Eifler-Lima, V. L. (2020). Geo-Measures: A PyMOL plugin for protein structure ensembles analysis. Computational Biology and Chemistry, 87, 107322. https://doi.org/10.1016/j.compbiolchem.2020.107322
   PubMed Web of Science ®Google Scholar
• Kambayashi, T., & Laufer, T. M. (2014). Atypical MHC class II-expressing antigen-presenting cells: Can anything replace a dendritic cell? Nature Reviews. Immunology, 14(11), 719–730. https://doi.org/10.1038/nri3754
   PubMed Web of Science ®Google Scholar
• 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/10.1021/jp003919d
   Web of Science ®Google Scholar
• Khatoon, N., Pandey, R. K., & Prajapati, V. K. (2017). Exploring Leishmania secretory proteins to design B and T cell multi-epitope subunit vaccine using immunoinformatics approach. Scientific Reports, 7(1), 8285. https://doi.org/10.1038/s41598-017-08842-w
   PubMed Web of Science ®Google Scholar
• Ko, J., Park, H., Heo, L., & Seok, C. (2012). GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Research, 40(Web Server issue), W294–297. https://doi.org/10.1093/nar/gks493
   PubMed Web of Science ®Google Scholar
• Kozakov, D., Beglov, D., Bohnuud, T., Mottarella, S. E., Xia, B., Hall, D. R., & Vajda, S. (2013). How good is automated protein docking? Proteins, 81(12), 2159–2166. https://doi.org/10.1002/prot.24403
   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/10.1038/nprot.2016.169
   PubMed Web of Science ®Google Scholar
• Krishnan G, S., Joshi, A., Akhtar, N., & Kaushik, V. (2021). Immunoinformatics designed T cell multi epitope dengue peptide vaccine derived from non structural proteome. Microbial Pathogenesis, 150, 104728. https://doi.org/10.1016/j.micpath.2020.104728
   PubMed Web of Science ®Google Scholar
• Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. (2001). Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. Journal of Molecular Biology, 305(3), 567–580. https://doi.org/10.1006/jmbi.2000.4315
   PubMed Web of Science ®Google Scholar
• Krüger, D. M., & Gohlke, H. (2010). DrugScorePPI webserver: Fast and accurate in silico alanine scanning for scoring protein-protein interactions. Nucleic Acids Research, 38(Web Server issue), W480–W486. https://doi.org/10.1093/nar/gkq471
   PubMed Web of Science ®Google Scholar
• Kyte, J., & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 157(1), 105–132. https://doi.org/10.1016/0022-2836(82)90515-0
   PubMed Web of Science ®Google Scholar
• Larsen, J. E. P., Lund, O., & Nielsen, M. (2006). Improved method for predicting linear B-cell epitopes. Immunome Research, 2(2), 2. https://doi.org/10.1186/1745-7580-2-2
   PubMedGoogle Scholar
• Laskowski, R. A., Jabłońska, J., Pravda, L., Vařeková, R. S., & Thornton, J. M. (2018). PDBsum: Structural summaries of PDB entries. Protein Sci, 27(1), 129–134. https://doi.org/10.1002/pro.3289
   PubMed Web of Science ®Google Scholar
• Laskowski, R., MacArthur, M., & Thornton, J. (2006). PROCHECK: Validation of protein-structure coordinates.
   Google Scholar
• Lee, S., & Nguyen, M. T. (2015). Recent advances of vaccine adjuvants for infectious diseases. Immune Network, 15(2), 51–57. https://doi.org/10.4110/in.2015.15.2.51
   PubMed Web of Science ®Google Scholar
• Lee, S.-M., Plieskatt, J., & King, C. R. (2018). Disulfide bond mapping of Pfs25, a recombinant malaria transmission blocking vaccine candidate. Analytical Biochemistry, 542, 20–23. https://doi.org/10.1016/j.ab.2017.11.009
   PubMed Web of Science ®Google Scholar
• Lindorff-Larsen, K., Piana, S., Palmo, K., Maragakis, P., Klepeis, J. L., Dror, R. O., & Shaw, D. E. (2010). Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins, 78(8), 1950–1958. https://doi.org/10.1002/prot.22711
   PubMed Web of Science ®Google Scholar
• Luckheeram, R. V., Zhou, R., Verma, A. D., & Xia, B. (2012). CD4&T cells: Differentiation and functions. Clinical & Developmental Immunology, 2012, 925135. https://doi.org/10.1155/2012/925135
   PubMedGoogle Scholar
• Magnan, C. N., Randall, A., & Baldi, P. (2009). SOLpro: Accurate sequence-based prediction of protein solubility. Bioinformatics (Oxford, England), 25(17), 2200–2207. https://doi.org/10.1093/bioinformatics/btp386
   PubMed Web of Science ®Google Scholar
• 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/10.1093/nar/gkn186
   PubMed Web of Science ®Google Scholar
• Mathews, D. H., Sabina, J., Zuker, M., & Turner, D. H. (1999). Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Journal of Molecular Biology, 288(5), 911–940. https://doi.org/10.1006/jmbi.1999.2700
   PubMed Web of Science ®Google Scholar
• Mathews, D. H., Turner, D. H., & Zuker, M. (2007). RNA secondary structure prediction. Current Protocols in Nucleic Acid Chemistry, 28, 11.2.1–11.2.17. https://doi.org/10.1002/0471142700.nc1102s28
   Google Scholar
• McDonald, I. K., & Thornton, J. M. (1994). Satisfying hydrogen bonding potential in proteins. Journal of Molecular Biology, 238(5), 777–793. https://doi.org/10.1006/jmbi.1994.1334
   PubMed Web of Science ®Google Scholar
• Mehla, K., & Ramana, J. (2016). Identification of epitope-based peptide vaccine candidates against enterotoxigenic Escherichia coli: A comparative genomics and immunoinformatics approach. Molecular bioSystems, 12(3), 890–901. https://doi.org/10.1039/c5mb00745c
   PubMedGoogle Scholar
• Meza, B., Ascencio, F., Sierra-Beltran, A. P., Torres, J., & Angulo, C. (2017). A novel design of a multi-antigenic, multistage and multi-epitope vaccine against Helicobacter pylori: An in silico approach. Infection, Genetics and Evolution, 49, 309–317. https://doi.org/10.1016/j.meegid.2017.02.007
   PubMed Web of Science ®Google Scholar
• Morris, A. L., MacArthur, M. W., Hutchinson, E. G., & Thornton, J. M. (1992). Stereochemical quality of protein structure coordinates. Proteins, 12(4), 345–364. https://doi.org/10.1002/prot.340120407
   PubMed Web of Science ®Google Scholar
• Nagpal, G., Usmani, S. S., Dhanda, S. K., Kaur, H., Singh, S., Sharma, M., & Raghava, G. P. (2017). Computer-aided designing of immunosuppressive peptides based on IL-10 inducing potential. Scientific Reports, 7, 42851. https://doi.org/10.1038/srep42851
   PubMed Web of Science ®Google Scholar
• Nogalski, M. T., Collins-McMillen, D., & Yurochko, A. D. (2014). Overview of human cytomegalovirus pathogenesis. Methods in Molecular Biology, 1119, 15–28. https://doi.org/10.1007/978-1-62703-788-4_2
   PubMedGoogle Scholar
• Nugent, T., Cozzetto, D., & Jones, D. T. (2014). Evaluation of predictions in the CASP10 model refinement category. Proteins, 82(Suppl 2), 98–111. https://doi.org/10.1002/prot.24377
   PubMed Web of Science ®Google Scholar
• Panda, S., & Chandra, G. (2012). Physicochemical characterization and functional analysis of some snake venom toxin proteins and related non-toxin proteins of other chordates. Bioinformation, 8(18), 891–896. https://doi.org/10.6026/97320630008891
   PubMedGoogle Scholar
• Pandey, R. K., Sundar, S., & Prajapati, V. K. (2016). Differential expression of miRNA regulates T cell differentiation and plasticity during visceral leishmaniasis infection. Frontiers in Microbiology, 7, 206. https://doi.org/10.3389/fmicb.2016.00206
   PubMed Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1982). Strain fluctuations and elastic constants. Journal of Chemical Physics., 76(5), 2662–2666. https://doi.org/10.1063/1.443248
   Web of Science ®Google Scholar
• Petersen, M. T., Jonson, P. H., & Petersen, S. B. (1999). Amino acid neighbours and detailed conformational analysis of cysteines in proteins. Protein Engineering, 12(7), 535–548. https://doi.org/10.1093/protein/12.7.535
   PubMedGoogle Scholar
• Plotkin, S. A., & Boppana, S. B. (2019). Vaccination against the human cytomegalovirus. Vaccine, 37(50), 7437–7442. https://doi.org/10.1016/j.vaccine.2018.02.089
   PubMed Web of Science ®Google 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, 514. https://doi.org/10.1186/1471-2105-9-514
   PubMed Web of Science ®Google 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
• Rappuoli, R. (2000). Reverse vaccinology. Current Opinion in Microbiology, 3(5), 445–450. https://doi.org/10.1016/S1369-5274(00)00119-3
   PubMed Web of Science ®Google Scholar
• Saadi, M., Karkhah, A., & Nouri, H. R. (2017). Development of a multi-epitope peptide vaccine inducing robust T cell responses against brucellosis using immunoinformatics based approaches. Infection, Genetics and Evolution, 51, 227–234. https://doi.org/10.1016/j.meegid.2017.04.009
   PubMed Web of Science ®Google Scholar
• Saha, S., & Raghava, G. P. (2006). AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Res, 34(Web Server issue), W202–209. https://doi.org/10.1093/nar/gkl343
   PubMed Web of Science ®Google Scholar
• Sarkar, B., Ullah, M. A., Araf, Y., & Rahman, M. S. (2020). Engineering a novel subunit vaccine against SARS-CoV-2 by exploring immunoinformatics approach. Informatics in Medicine Unlocked, 21, 100478. https://doi.org/10.1016/j.imu.2020.100478
   PubMedGoogle Scholar
• Schleiss, M. R. (2008). Cytomegalovirus vaccine development. Current Topics in Microbiology and Immunology, 325, 361–382. https://doi.org/10.1007/978-3-540-77349-8_20
   PubMed Web of Science ®Google Scholar
• Schleiss, M. R. (2010). Cytomegalovirus vaccines and methods of production (WO20009049138): The emerging recognition of the importance of virus neutralization at the epithelial/endothelial interface. Expert Opinion on Therapeutic Patents, 20(4), 597–602. https://doi.org/10.1517/13543770903584882
   PubMed Web of Science ®Google Scholar
• 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), W363–7. https://doi.org/10.1093/nar/gki481
   PubMed Web of Science ®Google Scholar
• Shey, R. A., Ghogomu, S. M., Esoh, K. K., Nebangwa, N. D., Shintouo, C. M., Nongley, N. F., Asa, B. F., Ngale, F. N., Vanhamme, L., & Souopgui, J. (2019). In-silico design of a multi-epitope vaccine candidate against onchocerciasis and related filarial diseases . Scientific Reports, 9(1), 4409. https://doi.org/10.1038/s41598-019-40833-x
   PubMed Web of Science ®Google Scholar
• Solanki, V., & Tiwari, V. (2018). Subtractive proteomics to identify novel drug targets and reverse vaccinology for the development of chimeric vaccine against Acinetobacter baumannii. Scientific Reports, 8(1), 9044. https://doi.org/10.1038/s41598-018-26689-7
   PubMed Web of Science ®Google Scholar
• The UniProt Consortium. (2015). UniProt: A hub for protein information. Nucleic Acids Research, 43(Database issue), D204–D212. https://doi.org/10.1093/nar/gku989
   PubMedGoogle Scholar
• Thomsen, M., Lundegaard, C., Buus, S., Lund, O., & Nielsen, M. (2013). MHCcluster, a method for functional clustering of MHC molecules. Immunogenetics, 65(9), 655–665. https://doi.org/10.1007/s00251-013-0714-9
   PubMed Web of Science ®Google Scholar
• Ullah, M. A., Sarkar, B., & Islam, S. S. (2020). Exploiting the reverse vaccinology approach to design novel subunit vaccines against Ebola virus. Immunobiology, 225(3), 151949.
   PubMed Web of Science ®Google Scholar
• Vadlapudi, A. D., Vadlapatla, R. K., & Mitra, A. K. (2012). Current and emerging antivirals for the treatment of cytomegalovirus (CMV) retinitis: An update on recent patents. Recent Patents on Anti-Infective Drug Discovery, 7(1), 8–18. https://doi.org/10.2174/157489112799829765
   PubMedGoogle Scholar
• Vajda, S., Yueh, C., Beglov, D., Bohnuud, T., Mottarella, S. E., Xia, B., Hall, D. R., & Kozakov, D. (2017). New additions to the ClusPro server motivated by CAPRI. Proteins, 85(3), 435–444. https://doi.org/10.1002/prot.25219
   PubMed Web of Science ®Google Scholar
• Vangone, A., & Bonvin, A. M. J. J. (2015). Contacts-based prediction of binding affinity in protein-protein complexes. eLife, 4, e07454. https://doi.org/10.7554/eLife.07454
   PubMed Web of Science ®Google Scholar
• Vita, R., Mahajan, S., Overton, J. A., Dhanda, S. K., Martini, S., Cantrell, J. R., Wheeler, D. K., Sette, A., & Peters, B. (2019). The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Research, 47(D1), D339–D343. https://doi.org/10.1093/nar/gky1006
   PubMed Web of Science ®Google Scholar
• Wang, S., Li, W., Liu, S., & Xu, J. (2016). RaptorX-Property: A web server for protein structure property prediction. Nucleic Acids Res, 44(W1), W430–435. https://doi.org/10.1093/nar/gkw306
   PubMed Web of Science ®Google Scholar
• Wang, P., Sidney, J., Kim, Y., Sette, A., Lund, O., Nielsen, M., & Peters, B. (2010). Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics, 11, 568. https://doi.org/10.1186/1471-2105-11-568
   PubMed Web of Science ®Google Scholar
• Weng, G., Wang, E., Wang, Z., Liu, H., Zhu, F., Li, D., & Hou, T. (2019). HawkDock: A web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA. Nucleic Acids Research, 47(W1), W322–W330. https://doi.org/10.1093/nar/gkz397
   PubMed Web of Science ®Google 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), W407–410. https://doi.org/10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• Wu, C. Y., Monie, A., Pang, X., Hung, C. F., & Wu, T. C. (2010). Improving therapeutic HPV peptide-based vaccine potency by enhancing CD4+ T help and dendritic cell activation. Journal of Biomedical Science, 17, 88. https://doi.org/10.1186/1423-0127-17-88
   PubMed Web of Science ®Google Scholar
• 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/10.1093/bioinformatics/btw514
   PubMed Web of Science ®Google Scholar
• Yazdani, Z., Rafiei, A., Valadan, R., Ashrafi, H., Pasandi, M., & Kardan, M. (2020). Designing a potent L1 protein-based HPV peptide vaccine: A bioinformatics approach. Computational Biology and Chemistry, 85, 107209. https://doi.org/10.1016/j.compbiolchem.2020.107209
   PubMed Web of Science ®Google Scholar
• Young, J. W., Locke, J. C. W., Altinok, A., Rosenfeld, N., Bacarian, T., Swain, P. S., Mjolsness, E., & Elowitz, M. B. (2011). Measuring single-cell gene expression dynamics in bacteria using fluorescence time-lapse microscopy. Nature Protocols, 7(1), 80–88. https://doi.org/10.1038/nprot.2011.432
   PubMed Web of Science ®Google Scholar
• Zhang, L. (2018). Multi-epitope vaccines: A promising strategy against tumors and viral infections. Cellular & Molecular Immunology, 15(2), 182–184. https://doi.org/10.1038/cmi.2017.92
   PubMed Web of Science ®Google Scholar
• Zhong, J., & Khanna, R. (2007). Vaccine strategies against human cytomegalovirus infection. Expert Review of anti-Infective Therapy, 5(3), 449–459. https://doi.org/10.1586/14787210.5.3.449
   PubMed Web of Science ®Google Scholar
• Zhu, J., & Paul, W. E. (2008). CD4 T cells: Fates, functions, and faults. Blood, the Journal of the American Society of Hematology, 112(5), 1557–1569.
   Google Scholar
• Zuker, M. (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research, 31(13), 3406–3415. https://doi.org/10.1093/nar/gkg595
   PubMed Web of Science ®Google Scholar