Multiple alignment of the NS3 protein sequences in HCV strains.

(PDF)</p

Final selected CTL, HTL and LBL epitopes for multi-epitope vaccines construction.

Final selected CTL, HTL and LBL epitopes for multi-epitope vaccines construction.</p

Multiple alignment of the P7 protein sequences in HCV strains.

(PDF)</p

S1 Fig -

Prediction of the secondary structure of the construct 1 (A) and construct 2 (B) vaccines. The predicted results showed that among 686 amino acids in the construct 1, 268 (39.07%), 135 (19.68%), 66 (9.62%) and 217 (31.63%) amino acids are involved in α-helix, extended strand, beta turn, and random coil, respectively. Our predicted outputs revealed that among 607 amino acids in the construct 2, 205 (33.77%), 132 (21.75%), 63 (10.38%) and 207 (34.10%) amino acids are involved in α-helix, extended strand, beta turn, and random coil, respectively. (DOCX)</p

Cytotoxic T Lymphocyte (CTL) epitopes of the P7protein.

(DOCX)</p

Various features of multi-epitope vaccines.

Various features of multi-epitope vaccines.</p

S2 Fig -

Linear (A and C) and Discontinuous (B and D) B-cell epitopes of the construct 1 (A and B) and construct 2 (C and D) vaccines (colored spheres). (DOCX)</p

Helper T Lymphocyte (HTL) epitopes of the NS5B protein.

(DOCX)</p

Prediction and assessment of the 3D structure of the multi-epitope vaccines.

(A) Schematic image of the final vaccine. (B) Ramachandran plot analysis of refined construct 1, showing 91.08%, 7.17% and 1.75% residues in favored, allowed and disallowed region, respectively, (C) ProSA validation of 3D construct 1, showing Z-score -3.28, (D) Ramachandran plot analysis of refined construct 2, showing 91.07%, 7.28% and 1.65% residues in favored, allowed and disallowed region, respectively, (E) ProSA validation of 3D construct 2, showing Z-score -3.88, (F and G) 3D structure of vaccines models showing α-helix (red cartoon), β-strand (yellow cartoon) and loop (green cartoon).</p

Multiple alignment of the NS5B protein sequences in HCV strains.

(PDF)</p