Table 2.

Number of protein pharmacophore elements selected for virtual screening using different pharmacophore models. “posHS” models were constructed using the hydration sites with positive estimated free energies. The hydration sites were also ranked in a descending order based on their estimated free energies. Top 25% (T0.25), 50% (T0.50), 75% (T0.75) and all (allHS) of the hydration sites were used to build hydration-site-restricted pharmacophore models. Two distance cutoffs, 1.0 Å and 1.5 Å, were used to select protein pharmacophore elements. The total number of protein pharmacophore elements in the binding site, i.e. the full protein pharmacophore (FPP) model, is also shown.

	fXa:1F0S (20)*		fXa:1MQ6 (33)		fXa:1NFU (30)		HIVPR:1AJV (26)		pcDHFR:1DAJ (27)
Distance Cutoff (Å)	1.0	1.5	1.0	1.5	1.0	1.5	1.0	1.5	1.0	1.5
posHS	7	16	9	25	8	18	8	15	16	30
T0.25	5	12	3	10	3	8	4	6	4	10
T0.50	7	16	7	18	6	11	6	12	7	17
T0.75	10	20	9	25	8	18	8	15	12	26
allHS	10	23	11	32	13	27	13	22	18	35
FPP	148		139		149		131		160

^*The values in the parentheses indicate the number of hydration sites identified for each protein system.