Table 1.

Virtual screening results using all protein pharmacophore elements (FPP). EF1: enrichment factors at 1% ranked decoys; EF10: enrichment factors at 10% ranked decoys; EF20: enrichment factors at 20% ranked decoys; AUC: area under the ROC curve. The number of protein pharmacophores and the runtime (seconds) per ligand needed in virtual screening are also shown for each system. The virtual screening was run on a single core of either 2.5GHz quad-core AMD2380 or 2.1GHz 12-core AMD6172 processors. On average, running the virtual screening on AMD2380 is faster than running on AMD6172 by about 18%.

	fXa:1F0S	fXa:1MQ6	fXa:1NFU	HIVPR:1AJV	pcDHFR:1DAJ
EF1	29.7	12.2	18.2	9.3	2.0
EF10	6.4	5.6	6.7	4.7	1.5
EF20	3.8	3.5	3.9	3.5	1.3
AUC	0.84	0.81	0.87	0.81	0.51
# of Protein Pharmacophores	148	139	149	131	160
Runtime per ligand (s)	1225	1468	1206	934	896