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Table 5 Results of the redocking experiments performed on the PPDbench dataset

From: Using parallelized incremental meta-docking can solve the conformational sampling issue when docking large ligands to proteins

PDB ID

DoFs

atoms

Vina

DINC

PDB ID

DoFs

atoms

Vina

DINC

2HO2

13

71

7.58 ±1.30

2.64 ±0.41

4B4N

40

110

8.82 ±0.95

5.21 ±0.61

2O9V

15

69

6.07 ±0.29

1.98 ±0.77

3AWR

41

84

8.25 ±0.74

4.94 ±0.37

3OBQ

19

62

7.50 ±0.70

2.52 ±0.93

2PEH

41

88

7.13 ±1.10

4.54 ±0.15

1CKA

22

65

6.78 ±0.18

2.68 ±0.49

2XVC

41

99

10.67 ±1.56

2.53 ±0.35

2A25

23

60

10.65 ±1.54

1.45 ±0.98

3GYT

42

81

7.14 ±0.47

5.63 ±0.30

2R9Q

24

59

5.93 ±0.72

2.25 ±0.22

1H6W

42

85

11.13 ±2.14

2.65 ±1.68

4H4F

25

72

3.75 ±0.20

1.05 ±0.03

2O4J

42

87

8.18 ±0.95

4.82 ±0.56

1SSH

25

76

8.31 ±1.04

5.04 ±0.30

4GQ6

42

99

6.98 ±1.36

4.65 ±0.28

3TJV

26

63

5.45 ±1.78

1.43 ±0.05

2XRW

42

100

9.19 ±1.24

6.26 ±0.67

3ERY

27

70

6.26 ±1.55

3.10 ±0.38

3DS4

42

103

7.85 ±0.82

4.79 ±0.36

3I5R

27

70

5.71 ±0.24

3.67 ±0.63

2PUY

43

80

8.94 ±2.46

3.94 ±0.30

1MFG

29

71

7.27 ±1.78

3.88 ±0.13

2P1T

43

86

5.86 ±1.09

4.05 ±0.74

1YWO

29

80

6.89 ±1.66

3.50 ±0.23

1D4T

44

90

14.65 ±1.08

4.81 ±0.87

1QKZ

30

62

5.63 ±1.71

2.82 ±0.39

2QSE

45

89

7.21 ±0.68

5.25 ±0.23

1K5N

30

64

4.66 ±0.99

2.84 ±0.63

1RXZ

45

97

7.35 ±0.81

3.53 ±0.91

1OAI

30

66

7.75 ±0.28

3.03 ±0.43

2BBA

45

115

7.18 ±0.82

5.08 ±0.35

1U00

30

71

7.01 ±1.08

2.20 ±0.15

1NQ7

46

90

8.06 ±0.41

5.46 ±0.30

1RST

30

76

7.16 ±0.36

4.37 ±0.14

3KMR

46

90

7.02 ±0.86

5.36 ±0.36

4GXL

30

81

7.41 ±1.01

2.69 ±0.20

3VTC

46

91

8.59 ±0.91

5.63 ±0.11

3RM1

31

71

6.23 ±0.88

3.21 ±0.63

2P54

46

97

7.40 ±0.75

5.14 ±0.34

2D0N

32

70

9.69 ±2.48

3.56 ±0.54

2QOS

46

97

7.64 ±0.37

5.89 ±0.33

2VR3

32

71

12.06 ±2.67

6.30 ±1.43

3RQG

47

92

7.09 ±0.29

5.34 ±0.24

4HTP

32

85

9.02 ±0.27

4.52 ±0.88

4ERY

47

100

7.19 ±0.33

3.61 ±0.59

2CE8

33

70

7.19 ±0.35

4.59 ±0.66

2FTS

47

104

8.04 ±0.42

4.54 ±0.24

4F1Z

33

72

15.69 ±2.99

2.88 ±0.17

1OW6

48

94

9.95 ±0.52

7.23 ±0.39

2ZJD

33

77

2.77 ±0.53

1.79 ±0.07

3C3R

48

104

8.94 ±1.47

5.87 ±0.34

3W1B

33

85

9.93 ±0.52

5.21 ±1.19

3L0E

49

98

7.08 ±1.09

5.22 ±0.10

3V2X

34

84

10.65 ±0.96

2.56 ±0.46

3OLF

49

99

6.51 ±0.57

5.49 ±0.27

3PTL

35

71

10.92 ±2.82

3.99 ±0.19

1T08

49

115

8.98 ±0.81

5.36 ±0.97

1X2R

35

74

6.51 ±0.95

4.12 ±0.40

1NLN

50

94

7.41 ±0.88

2.96 ±0.85

3KUS

35

83

7.28 ±1.99

2.53 ±0.57

4J8S

50

102

6.63 ±0.61

4.79 ±0.18

3U9Q

36

69

5.64 ±1.24

3.34 ±0.35

2FMF

50

107

9.26 ±0.85

6.54 ±0.33

1T7R

36

77

5.21 ±0.30

3.15 ±0.47

2FFF

50

109

7.98 ±0.52

4.72 ±0.77

2QBX

36

80

4.02 ±0.80

2.47 ±0.56

3QIS

50

109

5.91 ±0.44

3.85 ±0.49

1NX1

36

81

5.57 ±0.65

4.01 ±0.47

2PUX

50

111

9.27 ±1.71

5.18 ±0.28

2W2U

36

91

6.17 ±1.49

3.49 ±0.49

2CCH

51

102

8.26 ±0.45

4.94 ±0.81

1UJ0

37

74

7.02 ±1.10

3.89 ±0.40

2WHX

51

109

8.41 ±0.69

4.98 ±0.72

2HT9

37

85

7.72 ±0.75

5.74 ±0.23

2VWF

51

115

8.28 ±1.55

5.65 ±0.22

1EG4

37

106

8.97 ±0.86

4.64 ±0.26

2B9H

52

101

9.73 ±2.17

4.53 ±0.53

2FVJ

38

81

6.83 ±0.44

5.13 ±0.24

3UP3

53

108

8.75 ±0.83

6.28 ±0.19

3LL8

38

85

3.70 ±1.01

1.98 ±0.15

3H1Z

53

136

9.89 ±2.02

5.04 ±0.33

1T4F

38

86

7.52 ±0.81

5.27 ±0.13

1PZL

55

114

7.79 ±0.62

5.62 ±0.31

1TFC

39

81

7.02 ±0.64

4.95 ±0.28

4K0U

62

130

8.31 ±0.74

5.90 ±0.49

2DYP

39

81

3.70 ±0.91

1.71 ±0.12

2V8Y

67

129

9.10 ±1.42

6.09 ±0.36

1NTV

39

89

6.20 ±0.87

3.27 ±0.69

average

7.7 ±1.01

4.17 ±0.45

  1. For each complex in the dataset, we first list its identifier in the protein data bank (PDB ID), its number of rotatable bonds, i.e., degrees of freedom (DoFs), and its number of heavy atoms. Then, we list the average all-atom RMSD (over five replicates) associated with the top-RMSD conformation produced by Vina and DINC using their defaults parameters