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Table 6 Virtual Screening results for PDGFRβ at five different applicability levels

From: Estimation of the applicability domain of kernel-based machine learning models for virtual screening

Kernel

ADE

 

Threshold

AUROC

BEDROC (α)

Ligands

Decoys

     

100.00

53.6

32.2

20.0

  

OAK

KDE

50%

0.62

0.68

0.22

0.19

0.19

0.19

74

2789

  

33%

0.63

0.67

0.28

0.22

0.22

0.21

55

1854

  

200

0.667

0.78

0.80

0.65

0.64

0.57

7

193

  

100

0.673

0.79

0.95

0.83

0.82

0.72

6

94

 

wKDE

50%

0.62

0.68

0.22

0.19

0.18

0.19

74

2790

  

33%

0.63

0.67

0.28

0.22

0.22

0.21

56

1853

  

200

0.665

0.76

0.79

0.63

0.61

0.53

8

192

  

100

0.672

0.87

0.95

0.83

0.82

0.73

6

94

 

ONE

50%

-11.58

0.67

0.22

0.19

0.19

0.19

76

2781

  

33%

-10.95

0.66

0.26

0.20

0.20

0.19

58

1851

  

200

-8.93

0.78

0.80

0.65

0.64

0.57

7

192

  

100

-8.64

0.78

0.95

0.83

0.82

0.72

6

94

FlexOAK

KDE

50%

0.61

0.61

0.18

0.15

0.15

0.15

67

2796

  

33%

0.62

0.65

0.25

0.21

0.20

0.20

52

1857

  

200

0.647

0.84

0.79

0.61

0.60

0.53

9

191

  

100

0.653

0.87

0.95

0.82

0.80

0.70

7

93

 

wKDE

50%

0.61

0.61

0.18

0.15

0.15

0.15

61

2796

  

33%

0.62

0.65

0.25

0.20

0.20

0.20

52

1857

  

200

0.646

0.83

0.79

0.61

0.60

0.52

9

191

  

100

0.653

0.85

0.95

0.81

0.79

0.68

8

92

 

ONE

50%

-12.67

0.61

0.18

0.15

0.15

0.15

67

2796

  

33%

-12.04

0.65

0.25

0.20

0.20

0.20

50

1859

  

200

-10.33

0.82

0.79

0.61

0.59

0.52

9

191

  

100

-9.97

0.86

0.95

0.82

0.80

0.70

7

93

MARG

KDE

50%

0.83

0.37

0.13

0.11

0.11

0.11

52

2812

  

33%

0.84

0.40

0.18

0.17

0.17

0.17

25

1884

  

200

0.87

0.54

0.65

0.49

0.48

0.43

8

192

  

100

0.88

0.76

0.88

0.75

0.73

0.66

4

96

 

wKDE

50%

0.81

0.35

0.13

0.12

0.11

0.11

49

2814

  

33%

0.82

0.38

0.17

0.17

0.17

0.17

29

1880

  

200

0.86

0.57

0.65

0.49

0.48

0.42

8

192

  

100

0.87

0.86

0.91

0.82

0.81

0.77

3

97

 

ONE

50%

-5.05

0.39

0.13

0.11

0.11

0.11

51

2812

  

33%

-4.58

0.42

0.19

0.18

0.18

0.18

26

1883

  

200

-3.09

0.54

0.65

0.49

0.48

0.43

8

192

  

100

-2.79

0.85

0.91

0.82

0.81

0.77

3

97

  1. The threshold is adjusted such that either a certain fraction (50%, 33%) of the compounds or that exactly n compounds (n = 200, 100) remain in the domain. Results, which differ significantly from random rankings (p-Value < 0.01) are shown in bold.