Hierarchical clustering on the ligand data set.

Average hierarchical clustering based on pairwise ligand similarity for 269 ligands is performed using ChemMine [58]. The phylogenetic tree representing the 269 ligands in our data set is visualized using ITOL [56, 57]. A ligand that binds to a specific class of proteins is colored with the corresponding color of that class. Uncolored parts indicate ligands that bind to proteins from different classes or ligands that bind to proteins with no pre-defined class.