3.4  Molecular dynamics and simulation analysis
RMSD values and Atomic fluctuation per amino acid residue were obtained for Epitopes interacting with the HLA-Allele structure; this analysis allows a perfect pair selection and validation. Moreover, only two Epitope pairs, i.e., ITLCFTLKR and VYQLRARSV, were identified as probable T-cell epitopes and as putative vaccine specimens. Fig. 7 shows the RMSD Plot and Atomic fluctuation per residue for the ITLCFTLKR- HLA-A*68:01 complex, the RMSD Plot and Atomic fluctuation per residue for the VYQLRARSV- HLA-DRB1*07:01 complex. Both results were positive as best interactions, for protein-ligand docked complexes must possess RMSD values from 0 to 1.0 Å as a preferred range [13].
Fig. 7 A. RMSD Plot for ITLCFTLKR- HLA-A*68:01 complex, for each amino acid residue by Molecular dynamics analysis, B. B-Factor (atomic fluctuation) values per amino acid residue for Epitope ITLCFTLKR- HLA-A*68:01 docked complex, C. RMSD Plot for VYQLRARSV- HLA-DRB1*07:01, for each amino acid residue by Molecular dynamics analysis, D. B-Factor (atomic fluctuation) values per amino acid residue for Epitope VYQLRARSV- HLA-DRB1*07:01 docked complex.