The docking targets are Bacillus subtilis chorismate mutase (CM), human β 2 -adrenergic G proteincoupled receptor (β 2 AR), the DDR1 kinase domain (DDR1), and β -cyclodextrin (BCD). For the three proteins we use the 2CHT, 2RH1, and 3ZOS crystal structures from the Protein Data Bank , respectively. The proteins are prepared for docking with the Protein Preparation Wizard in the Maestro software by protonating all residues assuming pH 7 with PropKa. All three protein structures contain co-crystallized ligands: a transition state analog (TSA) for CM, carazolol for β 2 AR, and ponabtidin for DDR1. We redock these ligands to their respectively targets to get an idea of what docking score one would expect for known binders. We determined the protonation state and overall charge of each ligand (-2 for TSA, 0 for carazolol, and +1 for ponabtidin) by visual inspection of the crystal structure. In addition, we dock the known BCD-binder 6-(phenylamino)naphthalene-2-sulfonate (2,6-ANS) to BCD in the anionic form based on the typical pKa of the sulfonate group. The structures of the ligands are displayed in Table .