Fig. 3: Analysis of the SHAMAN probes.
From: Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN
A Violin plots representing the buriedness of the experimental pockets (y-axis) successfully identified by a given SHAMAN probe (x-axis). Buriedness values were extracted from the HARIBOSS database22 (Tab. S3 and S4, sample size n = 420). Each box represents the interquartile range between the first and third quartiles, with the median indicated by a horizontal black line. Outliers are marked as black diamonds. B Buriedness distribution for the RNA pockets occupied by ligands in all the structures deposited in HARIBOSS. C Total number of times that a probe explored an experimental binding site in the riboswitches of our validation set. D Cartoon representation of the 2’-deoxyguanosine (dG) riboswitch (PDB 3ski) with 2D structure of the GNG binder. In the dashed box, the 2D structures of the probes that identified the GNG binding site. E As in (C), for the viral RNAs of our validation set. F Cartoon representation of the RNA from the Hepatitis C Virus (PDB 3tzr) with 2D structure of the SS0 binder. In the dashed box, the 2D structures of the probes that identified the SS0 binding site.
