Table 4. Relative similarity indexes (κ, Equation 4) between different trajectories and pseudo-trajectories.
| DNA(n+p) | DNA(MD) | A-RNA(n) | A-RNA(MD) | |
|---|---|---|---|---|
| DNA(n) | 0.96 | 0.61 | 0.70 | 0.50 |
| DNA(n+p) | 1.00 | 0.61 | 0.71 | 0.63 |
| DNA(MD) | 1.00 | 0.62 | 0.61 | |
| A-RNA(n) | 1.00 | 0.69 |
The index n refers to naked B-DNA or A-RNA, and n+p refers to an extended set containing naked B-DNA and those distorted in protein–DNA complexes. MD eigenvectors were derived from trajectories of B-DNA and A-RNA26. Calculations were always performed considering 6mer duplexes. In the case of the DNA–protein complexes, only the 6mer DNA showing the largest distortion for each DNA–protein complex was introduced in the study.