Table 3.

Statistical results produced by the standard model of KGS2 and three variations in the in situ scoring test^a

Test set	Partner scoring function	Standard model of KGS2		Variation model 1		Variation model 2		Variation model 3
		Average reduced errorb	Applicable samples	Average reduced errorb	Applicable samples	Average reduced errorb	Applicable samples	Average reduced errorb	Applicable samples
HIV-1 protease (N = 303)	X-Score	0.41	227	0.41	227	−0.11	137	0.17	266
	ChemPLP	0.45	227	0.46	227	−0.12	137	0.11	266
	ASP	0.38	227	0.36	227	−0.22	137	0.08	266
	GoldScore	0.26	227	0.25	227	−0.29	137	0.03	266
Carbonic anhydrase 2 (N = 230)	X-Score	−0.05	189	−0.05	189	0.25	75	−0.04	203
	ChemPLP	−0.13	189	−0.13	189	0.25	75	0.00	203
	ASP	−0.10	189	−0.10	189	0.21	75	−0.02	203
	GoldScore	−0.10	189	−0.09	189	0.22	75	0.04	203
Beta-secretase 1 (N = 223)	X-Score	0.12	162	0.12	162	−0.09	9	−0.04	184
	ChemPLP	0.13	162	0.13	162	−0.15	9	−0.07	184
	ASP	0.14	162	0.14	162	−0.04	9	−0.07	184
	GoldScore	0.29	162	0.30	162	0.45	9	0.03	184
Beta-Trypsin (N = 196)	X-Score	0.33	157	0.33	157	0.37	66	0.05	164
	ChemPLP	0.47	157	0.46	157	0.55	66	0.24	164
	ASP	0.43	157	0.44	157	0.57	66	0.26	164
	GoldScore	0.59	157	0.60	157	0.71	66	0.39	164
Checkpoint kinase 1 (N = 61)	X-Score	0.00	37	0.00	37	−0.67	3	−0.10	48
	ChemPLP	0.00	37	0.00	37	−0.71	3	−0.00	48
	ASP	0.05	37	0.04	37	−0.70	3	0.06	48
	GoldScore	−0.01	37	−0.01	37	−0.61	3	0.07	48

^aThe similarity cutoff used in reference selection was 0.35 for all models listed in this table

^bAverage reduced error (in logK _a units) after application of KGS2, e.g. error by X-Score minus error by X-Score + KGS2. This value was computed among all applicable samples at the given similarity cutoff