Computational protocol: Exploring dengue genome to construct a multi-epitope based subunit vaccine by utilizing immunoinformatics approach to battle against dengue infection

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Protocol publication

[…] To study the physical basis of function and structure of biological macromolecules molecular dynamics (MD) simulation was used–. To understand the structural properties and interaction between receptor (TLR-3) and ligand (predicted vaccine protein) at the microscopic level, molecular dynamics simulation study was performed by using Gromacs v5.0. GROMOS96 43A1 force field and the particle mesh Ewald summation method was used to run full system MD simulation by Gromacs. Pdb2gmx was used to construct protein topology, which gives an idea about bonded and non-bonded characteristics. Here, the PRODRG2 server was used to generate ligand topology. Neutralization of system was performed by the addition of sodium and chloride ions in required quantity. Energy minimization was performed prior to simulation to ensure that the geometry of the system is appropriate and there are no steric clashes by the use of steepest descent algorithm approach. System equilibration was performed in a two-step process, the first step is NVT while another step is NPT ensemble, both steps use leapfrog algorithm. In the system, during equilibration steps, the temperature was raised up to 300 K and pressure up to 1 bar. After completion of system equilibration, a 10 ns molecular dynamics simulation was attained for trajectory analysis. […]

Pipeline specifications

Software tools GROMACS, PRODRG
Application Drug design