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Table 2 Docking success rate S 1 1 (in %) of ML SFs trained on Pr and tested on Cr complexes when characterized by different features.

From: Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins

Y (T)

Model

Feature set

  

X

A

R

G

XA

XR

XG

AR

AG

RG

XAR

XAG

XRG

ARG

XARG

Average

BA (1105)

MARS

28.72

20.00

5.13

18.46

34.36

36.92

28.21

21.03

16.41

8.21

37.95

28.72

40.00

8.21

36.41

24.58

 

RF

23.08

23.08

10.77

24.10

30.52

30.77

37.44

21.54

30.00

25.65

31.03

34.12

39.75

25.90

32.31

28.00

 

SVM

26.67

30.26

4.62

19.49

30.77

23.08

29.23

20.51

41.54

30.26

26.15

42.05

37.44

38.97

41.54

29.51

 

MLR

43.08

18.97

9.74

28.21

33.33

46.67

47.18

21.03

40.00

33.85

46.15

49.23

49.74

40.00

51.28

37.23

 

BRT

23.85

25.39

9.24

39.23

30.52

30.26

42.31

22.82

37.69

33.85

33.85

44.36

44.62

36.67

43.08

33.18

 

kNN

17.95

11.28

8.72

16.41

9.23

18.46

15.90

11.28

15.38

17.95

15.38

17.44

21.03

14.36

17.44

15.21

 

Average

27.22

21.50

8.04

24.32

28.12

31.03

33.38

19.71

30.17

24.96

31.75

35.99

38.76

27.35

37.01

27.95

RMSD (1105)

MARS

45.64

42.05

26.15

72.31

54.87

52.31

73.85

33.85

70.26

71.28

52.82

70.26

72.82

67.18

75.90

58.77

 

RF

32.72

32.31

13.85

67.39

39.80

42.26

70.36

32.10

64.82

68.10

41.95

64.82

72.00

64.51

67.18

51.61

 

SVM

29.74

28.72

6.15

66.15

37.95

30.77

70.77

32.31

61.54

56.41

45.64

64.10

62.05

58.97

63.08

47.62

 

MLR

44.62

35.90

6.15

70.26

58.46

54.36

72.31

40.51

70.26

65.64

56.92

75.90

70.26

67.69

69.23

57.23

 

BRT

38.77

34.87

8.10

70.98

52.00

41.13

74.77

35.59

67.70

69.02

48.92

71.39

72.51

65.33

67.49

54.57

 

kNN

31.79

24.10

3.08

55.38

30.77

17.44

62.56

15.90

40.00

38.97

22.05

44.62

45.13

37.95

41.03

34.05

 

Average

37.21

32.99

10.58

67.08

45.64

39.71

70.77

31.71

62.43

61.57

44.72

65.18

65.79

60.27

63.98

50.64

RMSD (1105x50)

MARS

44.10

31.79

5.13

72.82

62.56

49.74

75.38

34.87

73.33

70.77

64.10

76.92

72.31

72.31

78.97

59.01

 

RF

39.39

48.10

22.46

70.77

61.95

54.77

72.41

50.97

73.64

75.18

63.79

76.00

75.49

75.28

76.90

62.47

 

SVM

36.41

43.08

10.26

66.15

54.87

43.08

70.77

43.08

71.79

65.13

57.95

74.36

72.31

69.74

70.77

56.65

 

MLR

45.64

36.41

6.15

70.26

56.92

52.31

73.34

37.95

71.79

71.28

57.44

72.82

71.79

70.77

73.33

57.88

 

BRT

46.15

36.92

13.33

71.59

54.36

54.87

71.59

42.56

70.77

70.77

56.92

70.26

72.31

71.28

71.28

58.33

 

kNN

36.41

46.15

23.59

61.03

51.28

41.03

71.28

45.13

60.00

53.33

49.23

61.54

60.51

53.33

55.90

51.32

 

Average

41.35

40.41

13.49

68.77

57.01

49.30

72.46

42.43

70.22

67.69

58.24

72.05

70.68

69.23

70.63

57.61