Figure 5
From: Kissing loop interaction in adenine riboswitch: insights from umbrella sampling simulations
Analysis of interactions with alternative backward protocol Count of inter and intra-loop interactions in the 44 starting snapshots resulted from the different Apo US simulation initialization procedures. Results are shown for the 4 Apo runs, using the backward and forward protocols, both with k = 40(kcal/mol)/Å2 (I, II, respectively in orange and pale orange), and the two alternative backward protocols with the softer restraint (III in blue from protocol A, and IV in light blue from protocol B). Watson-Crick and non-Watson-Crick pairings as well as intra and inter-loop stackings are shown in the different panels.