Fig. 3.

Structural analysis and optimization of the ZL12138L vaccine. (A) Representation of the ZL12138L vaccine structure before and after structural optimization. The left panel shows the vaccine's initial structure, while the right panel illustrates the optimized structure, highlighting improvements in secondary and tertiary structural features. (B) Z-score distribution of residues in the initial ZL12138L vaccine structure, compared with X-ray and NMR reference datasets. The plot displays the Z-scores indicating structural deviations of individual residues relative to high-resolution structures. (C) Z-score distribution of residues in the optimized ZL12138L vaccine structure, compared with X-ray and NMR reference datasets. Post-optimization Z-scores demonstrated reduced structural deviations and improved stability. (D) Knowledge-based energy profile of the initial ZL12138L vaccine structure, calculated using different window sizes (10 and 40). Peaks in the energy profile indicate regions with higher energy and potential instability. (E) Knowledge-based energy profile of the optimized ZL12138L vaccine structure, highlighting energy minimization and increased stability across the sequence positions. (F) Ramachandran plot of the initial ZL12138L vaccine structure, showing the distribution of dihedral angles (phi and psi) for all residues. The plot identifies energetically favorable (dark red), allowed (yellow), and disallowed (white) regions. (G) Ramachandran plot of the optimized ZL12138L vaccine structure. Post-optimization, a greater proportion of residues fall within the most favored and allowed regions, reflecting improved structural quality and reduced steric clashes.