Skip to main content

Table 1 Results of the redocking experiments performed on the Dhanik dataset

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

PDB ID

DoFs

atoms

Vina

Vina100

12 Ă—Vina

24 Ă—Vina

DINC

288 Ă—Vina

DINC best

2FZC

7

18

3.51 ±0.45

3.54 ±0.20

2.80 ±0.31

2.77 ±0.24

2.76 ±0.24

2.24

2.24

1TYR

8

22

5.17 ±1.66

4.17 ±1.73

2.77 ±0.16

2.35 ±0.28

1.82 ±0.26

1.81

1.62

1V2O

10

30

3.53 ±0.07

3.27 ±0.22

2.65 ±0.23

2.58 ±0.19

2.39 ±0.18

2.17

2.17

2DRC

10

33

7.19 ±0.39

7.69 ±0.64

3.51 ±2.69

3.30 ±2.56

1.06 ±0.18

1.00

0.97

1NWL

11

31

5.31 ±1.08

5.19 ±1.82

3.03 ±0.61

2.23 ±0.50

1.49 ±0.11

1.61

1.18

1ELB

13

33

4.56 ±0.13

4.48 ±0.03

3.35 ±0.58

2.72 ±0.57

2.18 ±0.28

2.20

1.90

3GSS

18

39

5.29 ±1.09

4.96 ±0.70

3.15 ±1.12

2.73 ±0.97

3.10 ±0.20

1.74

1.61

1IS0

18

47

5.90 ±1.34

3.37 ±0.80

3.44 ±0.55

2.20 ±0.71

2.20 ±0.33

1.36

1.32

1A1B

19

39

3.03 ±0.28

3.18 ±0.47

2.40 ±0.40

1.97 ±0.53

1.97 ±0.41

1.27

1.27

1JQ9

20

47

7.99 ±2.20

9.51 ±0.21

5.41 ±1.39

5.48 ±1.77

2.90 ±0.15

2.46

2.46

4FIV

20

58

2.77 ±1.28

1.11 ±0.50

0.79 ±0.36

0.60 ±0.03

0.62 ±0.09

0.55

0.49

4ER2

22

48

3.42 ±0.45

2.40 ±0.75

2.30 ±0.60

1.98 ±0.49

1.55 ±0.09

1.35

1.33

1G7Q

22

57

3.99 ±1.35

2.01 ±1.15

2.23 ±1.01

1.48 ±0.20

1.10 ±0.07

1.11

0.98

1SLG

23

59

7.30 ±1.79

6.43 ±2.17

3.76 ±1.42

3.13 ±1.01

2.36 ±0.10

2.13

1.91

1FZK

23

68

6.64 ±0.72

3.94 ±1.84

4.26 ±1.76

1.94 ±0.62

1.20 ±0.15

1.37

1.11

2ER9

25

65

2.87 ±0.39

2.67 ±0.29

2.09 ±0.21

2.10 ±0.34

1.87 ±0.11

1.52

1.52

1FKN

29

63

4.67 ±1.27

3.56 ±0.38

3.08 ±0.14

2.83 ±0.22

2.11 ±0.28

2.08

1.75

1PZ5

29

67

5.54 ±0.81

6.28 ±0.10

4.69 ±0.73

4.49 ±0.22

3.16 ±0.29

3.90

1.87

1FO0

30

70

7.36 ±1.22

4.78 ±1.08

3.29 ±1.83

2.92 ±1.57

1.05 ±0.19

1.04

0.73

average

5.05 ±0.95

4.35 ±0.79

3.11 ±0.85

2.62 ±0.69

1.94 ±0.20

1.73

1.50

  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, Vina100, 12 ×Vina, 24 ×Vina, and DINC (see the “Results” section for explanations on these docking protocols), as well as the standard deviation. Finally, we list the all-atom RMSD associated with the top-RMSD conformation produced by 288 ×Vina and DINC best