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. 2015 Jan 20;5:7906. doi: 10.1038/srep07906

Figure 2. Projection of the loop3-4 conformational space simulated by cMD (left panel) and aMD (right panel) onto the two principal components (PC1 and PC2) produced from the PCA analysis of cMD and aMD trajectories.

Figure 2

The distributions of components are depicted with density-colored points, redder points denote higher density, while bluer points denote lower density. Matplotlib59 is used to generate these density-colored points. Structure a in the left panel indicated the open-loop conformation in cMD simulation, and structure b for an intermediate state. Structure c in the right panel represents the closed-loop conformation in aMD simulation, structure d for the loop-open state and structure e for an intermediate state sampled by aMD simulation.