Table 2.

Protein-Small molecules discriminatory success rates^a

Function	success rate (%)
	RMSD 0.0 Å	RMSD ≤0.5 Å	RMSD ≤1.0 Å	RMSD ≤1.5 Å	RMSD ≤2.0 Å
r·m·r·6	80	85	87	89	92
DrugScoreCSD	77	82	83	85	87
ITScore	64b	67b	72	79	82
Cerius2/PLP	52	58	63	69	76
Cerius2/LigScore	48	58	64	68	74
SYBYL/F-Score	38	47	56	66	74
DrugScorePDB	49	58	63	68	72
Lennard-Jones	57	61	65	66	68
Cerius2/LUDI	23	33	43	55	67
X-Score	25	33	40	54	65
AutoDock	8	19	34	52	62
DFIRE	-	-	37	52	58
DOCK/FF	n/ab,c	18b	37	47	58
Cerius2/PMF	32	35	40	46	52
SYBYL/G-Score	13	15	24	32	42
SYBYL/ChemScore	7	8	12	26	35
SYBYL/D-Score	3	3	8	16	26

^aThe success rate at each RMSD criterion is the percentage of all protein-small molecule complexes with the best (i.e., lowest) scoring complex having an RMSD to the native conformation within the allowed deviation. The RMSD ≤0.5Å column corresponds to the definition of ‘accurate’ discrimination used in Figure 1.

^bHuang, S. Personal communication. 15 Feb 2008.

^cThe success rate for DOCK/FF at RMSD 0.0Å is not available as the minimization in DOCK changes the small-molecule position prior to scoring. The r·m·r function outperforms all other functions at distinguishing native and near-native biomolecular interactions from incorrect conformations.