Figure 8:
Comparison of the motif-strengthening mutants with the wildtype systems. For 3_6 pseudoknot, both the 77-nt (SimRNA) and 144-nt (RNAComposer) PSM are shown in cartoon mode with their wildtype systems aligned in mesh (by PyMol48 for the 77-nt region). The mutations are highlighted as spheres in PSM structure and labeled. The 2D structure comparison is also provided with PSM at top and wildtype at bottom. Comparisons for the 77-nt 3_3 PSM (iFoldRNA) and 77-nt 3_5 mutant (SimRNA) are shown in similar manner.