Fig. 3.

Probability distribution of the first principal component (PC1) and PC1’s trajectories along time evolution. PC1 was obtained from dPCA using $\mathrm{C}\alpha$ atoms of the active site. Blue and orange lines are for protomer A and B, respectively. (A) SARS-CoV 3CL^pro (1UJ1), (B) SARS-CoV 3CL^pro (1UK3), (C) SARS-CoV-2 CoV 3CL^pro (HM), and (D) SARS-CoV-2 3CL^pro (6LU7). (E) The $\mathrm{C}\alpha$ atoms of the active site that was used in dPCA. PC1 of each graph was not identical to each other, i.e., we analyzed each Traj i (i=1,2,…,10) individually in the dPCA, because merging multiple trajectories results in the expansion of conformational space, leading to the poor capability of dPCA to discriminate conformations.