Probing Riboswitch Binding Sites with Molecular Docking, Focused Libraries, and In-line Probing Assays

Molecular docking calculations combined with chemically focused libraries can bring insight in the exploration of the structure–activity relationships for a series of related compounds against an RNA target. Yet, the in silico engine must be fueled by experimental observations to drive the research into a more effective ligand-discovery path. Here we show how molecular docking predictions can be coupled with in-line probing assays to explore the available chemical and configurational space in a riboswitch binding pocket.