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Table 3 Statistical results produced by the standard model of KGS2 and three variations in the in situ scoring testa

From: Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints

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

  1. aThe similarity cutoff used in reference selection was 0.35 for all models listed in this table
  2. 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