Fig. 3.

Folding kinetics comparison between BHG${}^{°}$ (top) and BHG${}^{\psi }$ (bottom) of the preQ₁ riboswitch (Bsu, left), the Ribosomal RNA from E.coli (PDB_00702, middle), and the signal recognition particle RNA (SRP_00094, right). The process was started in the open chain structure and run until convergence to the thermodynamic equilibrium distribution except the case of PDB_00702 on BHG${}^{°}$ where the equilibrium was still not reached until 10¹⁸ arbitrary time units. Dotted vertical line indicates when the simulation reaches its equilibrium. The LMs that appear in both kinetics plots are marked with same color, otherwise pseudoknot-free and pseudoknotted LMs are marked with black and red, respectively. The sums of the structure probabilities of pseudoknot-free and pseudoknotted LMs on BHG${}^{\psi }$ are marked with blue and red dashed lines, respectively (Color version of this figure is available at Bioinformatics online.)