Superposition of the predicted and the experimental structures for four types of loops.

<p>The experimental structures are colored red, the predicted loops are green, and the first 20 structures in the largest cluster are colored light-blue and semi-transparent. The anchor nucleotides are colored magenta. (A) to (H) correspond to the data points of the same labels shown in <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005032#pcbi.1005032.g007" target="_blank">Fig 7</a>. (A)(B) are hairpin loops, (C)(D) internal loops, (E)(F) three-way junction loops, (G)(H) four-way junction loops. The loop length and RMSD are as follows: (A) 9 nt and 4.21 Å, (B) 17 nt and 6.46 Å, (C) 9 nt and 3.81 Å, (D) 17 nt and 3.76 Å, (E) 9 nt and 4.51 Å, (F) 17 nt and 4.34 Å, (G) 9 nt and 3.96 Å, (H) 17 nt and 5.17 Å.