FIGURE 3.

Frequency distribution and corresponding initial potential for the four different energy terms (Loop–loop distance [cf. subsection “Loop–loop interaction energy”], radius of gyration [cf. subsection “Radius of gyration”], and A-minor energy for interior and hairpin loops [cf. subsection “A-minor energy”]). The target (dashed) and reference (dotted) distributions are obtained from subgraphs of the native ribosome and a decoy ribosome structure obtained by simulating using only constraint energies (i.e., clash detection and junction closure), respectively. Here we used subgraphs of length 83, the length of the Escherichia coli thi-box riboswitch 2HOJ.