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. 2016 Jan 19;110(2):455–469. doi: 10.1016/j.bpj.2015.12.010

Figure 2.

Figure 2

Assessment of the connector loops refinement by principal component analysis (PCA). (A) Projection of simulated annealing runs onto the first and second principal components (PC1 and PC2) obtained after performing PCA on the SAMD trajectory (squares). The semicircular arrow shows conformational changes during the SAMD simulation. Five high temperature conformations P1, P2, P3, P4, and P5 (red circles) were selected from the trajectory and cooled down to 300 K. Dense clusters (blue symbols) labeled with P1c, P2c, P3c, P4c, and P5c were obtained after cooling. (B) Comparison of the initial loop model (blue) with refined loops after SA runs (red) interacting with the DNA backbone (cyan) in the channel center.