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. Author manuscript; available in PMC: 2019 Apr 29.
Published in final edited form as: J Comput Chem. 2018 Oct 11;39(28):2360–2370. doi: 10.1002/jcc.25571

Figure 6.

Figure 6

Illustration of the first two principal components (panels A-E) obtained by doing the PCA of the snapshots of the Ku heterodimer bound to DNA collected from the all-atom MD simulations. The principal components are represented by arrows colored green (A), red (B), orange (C), blue (D), and purple (E), respectively. The structure displayed in a given panel has been obtained by adding the respective eigenvector coordinates to the site coordinates; the deviations from the average structure are marked by coloring the respective parts of the system from blue (low deviations) to deep red (high deviations). On the right side of each panels, the the squares of Cα-atom the fluctuations corresponding to a given component are plotted.