Fig 4 -

(A) Ramachandran plot analysis based on final vaccine epitopes showing 83.2%, 15.3%, 0.8% and 0.8% of protein residues in favored, additional allowed, generously and disallowed (outlier) area region respectively. (B) ProSA-web results indicated a Z-score of– 2.71. The z-score of protein vaccine is showed in large black spot. Z-score plot consists the Z-scores of all experimentally protein chains in PDB determined by nuclear magnetic resonance (NMR) spectroscopy (dark blue) and X-ray crystallography (light blue). (C) Validation of the vaccine structure by ERRAT with a score of 91.156.</p

Displays the second and 3D of the designed multi-epitope vaccine.

(A) The alpha helix residues are in pink, the beta- strand residues are in yellow and the coil residues are in grey. The predicted secondary structure indicates that the final vaccine constitutes 21.84% alpha-helix, 16.09% beta-strand, and 62.07% coil, respectively. (B) The 3D structure of the designed vaccine construct. (C) Model of the 3D structure of the refined vaccine by the GalaxyRefine server.</p

Quality scores of 5 models predicted by GalaxyRefine server.

Quality scores of 5 models predicted by GalaxyRefine server.</p

The molecular dynamics simulation of the vaccine-TLR4 docked complex.

(A) Main-chain deformability simulation, the hinges are regions with high deformability. (B) B-factor values calculated by normal mode analysis, quantifying the uncertainty of each atom. (C) The eigenvalue of the docked complex, showing the energy required to deform the structure. (D) The covariance matrix between pairs of residues (red: correlated, white: uncorrelated, blue: anti-correlated). (E) The elastic network model, suggesting the connection between atoms and springs. The springs are more rigid if their greys are darker.</p

Most probable predicted epitopes with MHC class II alleles from IEDB analysis tool.

Most probable predicted epitopes with MHC class II alleles from IEDB analysis tool.</p

Hydrophobic and hydrogen bond forming residues in the best docked conformations.

Hydrogen bonds and salt bridges are shown with green and red dashed lines, respectively. Half circle in red color indicates the residues involved in hydrophobic interactions.</p

The solubility analysis of the vaccine construct by Protein-Sol server was predicted to be 0.679.

The solubility analysis of the vaccine construct by Protein-Sol server was predicted to be 0.679.</p

Prediction of mRNA secondary structure of multi-epitope vaccine by RNAfold server.

Prediction of mRNA secondary structure of multi-epitope vaccine by RNAfold server.</p

Global energy designated from the top ten results by the FireDock server.

Global energy designated from the top ten results by the FireDock server.</p

Most conserved B cell epitope sequences predicted by these two methods (BCPREDS and ABCpred).

Most conserved B cell epitope sequences predicted by these two methods (BCPREDS and ABCpred).</p