title: Probing riboswitch binding sites with molecular docking, focused libraries, and in-line probing assays.
abstract: 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.
authors: Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy.
authors: Francesco
authors: F
authors: Colizzi
authors: Anne-Marie
authors: AM
authors: Lamontagne
authors: Daniel A
authors: DA
authors: Lafontaine
authors: Giovanni
authors: G
authors: Bussi
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D008024:Ligands; D008967:Molecular Biology / Q000379:methods; D062105:Molecular Docking Simulation; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D058928:Riboswitch / Q000235:genetics*; D013329:Structure-Activity Relationship
chemical_list: D008024:Ligands; D058928:Riboswitch; D012313:RNA