Structural analysis of antigenic variation and adaptive evolution of the H5N1 neuraminidase gene
Fig 6
Cα RMSD Analysis: Time Evolution and Ensemble Distribution.
The RMSD was calculated for the Cα atoms of the backbone relative to the energy-minimized structure of the WT protein. (A) Plots the RMSD (nm) over the first of the trajectory, illustrating the overall structural stability and convergence of the backbone. (B) Displays the KDE of the entire ensemble (300 ns total simulation). The KDE represents the probability density of sampling specific conformations, where the vertical dashed lines indicate the Mean for each system, visually confirming the statistically significant shifts in the ensemble (Table 3).