Small molecule-protein docking Small molecule-protein docking is an essential computational technique in structural biology and drug development. It aims to ascertain the binding modes and affinities inside the binding site of small compounds or ligands, thereby guiding their binding to a target protein( ) (Figure ). Examples of small molecule docking programs are AutoDock ( ), BetaDock ( ), PLANTS ( ), and GalaxyDock3 ( ). Also, rational drug design depends on this method since it provides essential knowledge on the molecular interactions between ligands and proteins.