Structural basis of development of multi-epitope vaccine against Middle East respiratory syndrome using in silico approach

Srivastava, Sukrit; Kamthania, Mohit; Singh, Soni; Saxena, Ajay K; Sharma, Nishi

AutoDock Tool 4.2 and AutoDock Vina were used for molecular docking study of the selected epitopes and their respective HLA allele binders. 45, 46 Further, the docked complexes were subjected to MD simulation study by Gromacs 5.1.4 using Optimized Potentials for Liquid Simulations -all atom (OPLS-AA) force field. 47, 48 Molecular interaction analysis (docking) of the selected cTl epitopes with TaP Molecular docking study of the shortlisted CTL epitopes with TAP receptor was performed by AutoDock Vina. 45, 46 For more accurate prediction, instead of homology modeling, the cryo-EM structure of TAP (PDB ID: 5u1d) was used. 49 For docking, the antigen from the TAP cavity of the original structure was removed.