Scrutinizing the SARS-CoV-2 protein information for the designing an effective vaccine encompassing both the T-cell and B-cell epitopes

Neha Jain; Uma Shankar; Prativa Majee; Amit Kumar

Proteinprotein docking of immune receptor TLR3 and the constructed vaccine was carried out using ClusPro server. In total 30 TLR3-vaccine construct complexes were generated. The The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.26.009209 doi: bioRxiv preprint standard molecular dynamics simulation studies using NAMD suite. The 10,000 steps energy minimization of the complex lead to the generation of a minimized energy complex with energy of -756791.5601 Kcal/mol ( Figure 8C ). After subsequent heating the system from 0 K to 310 K, the temperature was kept constant throughout ( Figure 8D) . Energy plots depicted no major changes throughout the simulation ( Figure 8E -G and Supplementary Figure S5 ). RMSF analysis of the complex showed a mobility region at ~740 th residue and ~1100 residue of the TLR3-vaccine complex ( Figure 8H ). On trajectory analysis, the RMSD plot was constructed that revealed the major deviations during the initial 1.5 ns, thereafter the system remained constant till 10 ns.