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.
Search related documents:
Co phrase search for related documents- DCD file and energy total potential kinetic change: 1
- DCD file and molecular dynamic: 1
- DCD file and ns simulation: 1
- DCD file and real environment: 1
- DCD file and real environment stability: 1
- dynamic tool and molecular dynamic: 1
- dynamic tool and molecular dynamic tool: 1
- energy minimization and molecular dynamic: 1, 2
- energy minimization and ns simulation: 1, 2, 3, 4
- energy minimization and real environment: 1
- energy minimization and real environment stability: 1
- energy total potential kinetic change and molecular dynamic: 1
- energy total potential kinetic change and ns simulation: 1
- energy total potential kinetic change and real environment: 1
- energy total potential kinetic change and real environment stability: 1
- molecular dynamic and ns simulation: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
- molecular dynamic and real environment: 1
- molecular dynamic and real environment stability: 1
- ns simulation and real environment: 1
Co phrase search for related documents, hyperlinks ordered by date