Figure 4.
Two examples showing the roles of DI-restrains in RNA 3D structure optimization. A–D and E–H are the contact maps, 2D structures, 3D structures optimized without and with DI restraints for RNAs 4LVV and 3U4M, respectively. Cnat, Cnrs and Crs denote the contacts in the native structure and the structures optimized without and with DI restraints, respectively; DI* are the top L DIs but with the isolated points removed; The red circle and rectangular box are the regions of the pseudoknot and tertiary interactions, respectively. The red regions in the 3D structures are residues that would form pseudoknot or tertiary interactions. The 2D and 3D structures are generated by Forna (40) and PyMOL (41), respectively.