The 3D structures (upper) and core base-interaction patterns (lower) of four predicted kink-turn related motif instances. All RNA 3D structure figures were generated using PyMol (http://www.pymol.org). These instances are ranked at the sixth (A), ninth (B), tenth (C), and fifteenth (D) in the RNAMotifScanX top list. All instances show sharp turns between the helices, but no significant kinks. The arrows shown in the top panel indicate the directions of the two helices, where the sharp turn between them is a key feature of the kink-turn motif. Motif instances shown in A and B are rediscovered from FR3D's predictions (cyan arrows), while motif instances shown in C and D are newly discovered by RNAMotifScanX (magenta arrows). Even though these instances share similar 3D structures, their base-interaction patterns vary. The lower panel shows the core interactions (which correspond to the colored residues in the upper panel) of the instances that are locally aligned to the query. The aligned interactions are different among the four instances, but all of them share a core that consists of two shared pairs and a connecting outward stacking interaction (boxed regions).
