Author: Neha Jain; Uma Shankar; Prativa Majee; Amit Kumar
Title: Scrutinizing the SARS-CoV-2 protein information for the designing an effective vaccine encompassing both the T-cell and B-cell epitopes Document date: 2020_4_1
ID: lmstdmyb_36
Snippet: The refined modelled structure of the multi-epitope vaccine construct was further evaluated for its stability in the real environment by simulating it in a water sphere using NAMD-standard molecular dynamics tool (https://www.ks.uiuc.edu/Research/namd/) by using parallel processors. The required structure files (.psf) were generated by psfgen using Visual Molecular Dynamics (VMD) tool v.1.9.3 by utlizing CHARMM force fields for proteins. Initiall.....
Document: The refined modelled structure of the multi-epitope vaccine construct was further evaluated for its stability in the real environment by simulating it in a water sphere using NAMD-standard molecular dynamics tool (https://www.ks.uiuc.edu/Research/namd/) by using parallel processors. The required structure files (.psf) were generated by psfgen using Visual Molecular Dynamics (VMD) tool v.1.9.3 by utlizing CHARMM force fields for proteins. Initially, a 10,000 steps energy minimization was performed followed by subsequent heating the system from 0 K to 310 K. Thereafter, a 20 ns standard molecular dynamics was performed and trajectory DCD file generated was used to evaluate RMSD. The change in kinetic, potential and total energy was evaluated for these 20 ns simulation using VMD.
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