Table 2.

Optimal settings of Gold for redockings of seven reference inhibitors.

Complex	Binding site-radius (Å)	Water molecules	Scoring function	Value of scoring function	rmsd (Å)
1EVE	10	1159, 1249, 1254 (toggle *)	ChemScore	49.48	0.8
1ACJ	12	616, 634, 643 (toggle)	GoldScore	67.95	0.4
2CKM	10	None	GoldScore	80.72	1.3
1DX6	12	None	GoldScore	59.34	0.6
1ACL	10	None	GoldScore	40.45	1.6
1AX9	12	None	ChemScore	26.36	1.4
1VOT	12	619, 680 (toggle)	ChemScore	41.60	0.9

^*The program decides at the step of docking if the water molecule is engaged in ligand binding.