Fig. 2: Assessment of the SHAMAN accuracy.
From: Identifying small-molecules binding sites in RNA conformational ensembles with SHAMAN
A A cartoon-surface representation of the four riboswitches in our benchmark set (Tab. S1), with the corresponding name in the upper left of each panel. In the lower part, the PDB id of the starting structure used in our SHAMAN simulations is reported in a brown and cyan box for the holo-like and apo case (when available), respectively. The cartoon representations correspond to the holo-like structures. B As in panel (A), for the three viral RNAs of our benchmark set (Tab. S1). C Definition of the validation distance (Eq. 10) as the distance between the free-energy weighted center of an interacting site and the center of mass of the experimental ligand. D \(\varDelta \varDelta G\) distribution of the probes that correctly identified known experimental pockets for holo-like (brown) and apo simulations (cyan). E Scatter plots of the validation distance (x-axis) and cutoff defined by Eq. 10 (y-axis) for holo-like (brown, upper panel) and apo (cyan, lower panel) simulations. The dashed line indicates validation distances equal to the validation cutoff, while the dotted line corresponds to half the validation cutoff. Each system is identified by a different marker shape, as defined in the legend.
