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Table 1 This table shows the results for the 28 complexes in the test set

From: Protein docking with predicted constraints

 

Unbound

Bound

PDB ID

500

1000

2000

5000

500

1000

2000

5000

1gla

0 / 0

0 / 0

0 / 0

0 / 0

1 / 1

2 / 2

2 / 4

7 / 8

1y64

0 / 0

0 / 0

0 / 0

0 / 0

0 / 1

0 / 2

0 / 2

0 / 3

1akj

10 / 3

13 / 5

15 / 6

26 / 13

5 / 5

8 / 8

14 / 12

18 / 21

1s1q

0 / 0

0 / 0

0 / 0

0 / 0

4 / 12

5 / 16

6 / 30

8 / 41

3bp8

4 / 0

5 / 2

9 / 4

27 / 14

9 / 8

10 / 13

12 / 25

18 / 42

1pvh

0 / 0

0 / 0

0 / 0

0 / 0

2 / 1

2 / 1

3 / 2

5 / 3

2nz8

1 / 1

1 / 1

3 / 2

4 / 3

23 / 9

38 / 10

50 / 12

70 / 23

2j0t

2 / 2

3 / 2

7 / 3

11 / 7

10 / 5

12 / 5

20 / 8

30 / 20

7cei

0 / 1

0 / 1

0 / 1

0 / 4

5 / 1

6 / 1

7 / 1

7 / 1

1ijk

0 / 0

0 / 0

0 / 0

1 / 1

2 / 2

2 / 2

3 / 3

5 / 5

2o3b

0 / 0

0 / 0

0 / 0

10 / 4

0 / 0

0 / 0

0 / 0

1 / 1

1jwh

0 / 0

1 / 0

5 / 0

9 / 1

0 / 0

0 / 0

0 / 0

3 / 0

1i2m

0 / 0

0 / 0

0 / 0

3 / 0

1 / 1

3 / 1

6 / 3

12 / 6

2pcc

2 / 0

3 / 0

4 / 1

8 / 1

2 / 0

5 / 5

8 / 6

15 / 13

1h1v

0 / 0

0 / 0

0 / 0

0 / 0

2 / 2

3 / 3

5 / 6

10 / 8

1b6c

0 / 0

1 / 1

2 / 1

2 / 1

21 / 25

36 / 35

62 / 43

117 / 61

2hle

1 / 0

2 / 1

3 / 1

11 / 3

2 / 0

4 / 0

9 / 2

16 / 5

1bkd

0 / 0

0 / 0

0 / 0

0 / 0

19 / 6

35 / 9

67 / 15

106 / 20

1he1

11 / 6

18 / 12

30 / 17

53 / 34

32 / 3

42 / 5

77 / 9

140 / 17

1m10

16 / 5

19 / 5

27 / 11

54 / 17

36 / 9

54 / 14

75 / 17

106 / 22

1i4d

0 / 0

0 / 0

0 / 0

0 / 0

4 / 7

5 / 8

9 / 11

13 / 22

1azs

0 / 0

0 / 0

0 / 0

0 / 0

16 / 2

24 / 2

48 / 3

58 / 7

2sni

1 / 1

1 / 2

1 / 3

3 / 16

26 / 14

41 / 26

70 / 38

142 / 82

1gpw

0 / 1

2 / 1

2 / 3

13 / 10

25 / 14

42 / 22

73 / 26

132 / 41

1ofu

3 / 0

4 / 0

6 / 1

10 / 1

7 / 0

18 / 0

38 / 2

75 / 4

1z0k

1 / 1

3 / 1

16 / 4

39 / 20

36 / 17

58 / 27

92 / 43

179 / 85

1jzd

0 / 0

0 / 0

1 / 0

2 / 4

29 / 7

44 / 13

67 / 14

110 / 27

1fak

0 / 0

0 / 0

0 / 0

1 / 0

0 / 1

1 / 2

6 / 4

11 / 6

Av. gain

2,48

2,24

2,26

1,86

2,09

2,15

2,43

2,38

  1. The top five complexes are those for which no true contact was ranked in the highest ranking 100 predicted contacts and had no correct constraints among the 100 used in docking. Unbound and bound docking runs are split into several columns for different numbers of models retained, and each cell shows the number of acceptable models using constraints and without constraints. The bottom row shows the average gain in acceptable models in each case, given by the total number of acceptable models using constraints divided by the total without constraints (including all complexes, even those without correct constraints).