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Table 4 Comparison with HEX on unbound cases of Benchmark 2.0.

From: Protein-protein docking using region-based 3D Zernike descriptors

  

HEX

 

ZDOCK

LZerD

Complex

Rank

lRMSD

HITS2K

Rank

lRMSD

HITS2K

Rank

lRMSD

HITS2K

1ACB

694

8.3

3

185

9.98

5

21

9.98

2

1AHW

234

8

3

34

9.86

20

5

2.68

43

1AKJ

209

9.6

10

-

-

-

-

-

-

1AVX

108

8.9

7

604

9.43

4

-

-

-

1AY7

645

9.9

4

568

9.39

11

1884

6.13

1

1B6C

593

9

2

182

5.6

10

73

6.2

10

1BUH

743

7.7

2

-

-

-

599

9.73

1

1BVK

-

-

-

70

7.56

 

1125

9.83

10

1BVN

63

9.1

20

29

8.65

52

2

6.89

49

1CGI

42

9.4

17

145

3.88

32

86

8.13

12

1D6R

447

7.7

1

303

8.44

3

344

7.84

8

1DE4

946

8.6

1

-

-

-

-

-

-

1DFJ

17

9.5

14

5

6.64

67

-

-

-

1DQJ

-

-

-

152

9.82

23

-

-

-

1E6E

109

5.6

10

-

-

-

52

4.49

10

1E6J

-

-

-

12

5.34

93

87

9.97

20

1E96

-

-

-

-

-

-

1375

8.91

1

1EAW

9

5

20

3

5.43

87

6

9.95

19

1EER

609

9.2

8

-

-

-

-

-

-

1EWY

76

9.1

12

22

8.08

51

103

9.91

110

1EZU

-

-

-

-

-

-

815

7.89

3

1F34

124

6.7

11

5

5.45

20

-

-

-

1F51

371

9.6

5

602

9.78

4

1101

8.31

1

1FQJ

41

8

12

-

-

-

1014

9.63

3

1FSK

5

1.8

16

1

4.04

149

15

6.23

28

1GHQ

-

-

-

-

-

-

1571

9.14

1

1GRN

914

9.1

2

1704

5.81

2

1407

7.41

2

1HE1

37

6.4

18

23

8.14

8

47

6.2

7

1HIA

51

8.7

6

-

-

-

1

9.49

74

1I4D

-

-

-

-

-

-

286

9.11

2

1I9R

82

2.1

8

104

9.07

16

104

9.41

10

1IJK

1012

8.7

3

-

-

-

-

-

-

1IQD

-

-

-

492

8.99

11

41

6.46

27

1JPS

-

-

-

171

8.51

7

292

2.01

20

1K4C

21

9.6

1

-

-

-

219

9.78

6

1KAC

687

8.7

1

-

-

-

655

3.95

3

1KXP

36

9.4

13

1616

7.11

2

1226

8.05

1

1KXQ

488

7.1

5

116

7.58

29

73

4.33

16

1M10

514

9.5

2

-

-

-

-

-

-

1MAH

2

1.2

20

92

3.86

9

92

2.43

2

1ML0

-

-

-

36

2.87

35

121

5.71

2

1MLC

408

3.6

2

110

6.17

12

1834

4.48

1

1NCA

116

1.2

5

14

7.08

49

270

9.97

2

1NSN

142

1.5

6

185

5.07

19

94

8.61

4

1PPE

2

9.7

47

1

0.86

358

1

2.26

184

1QA9

-

-

-

-

-

-

546

8.07

6

1QFW

-

-

-

257

8.63

4

108

9.54

2

1TMQ

356

5.9

9

314

6.12

11

50

3.71

11

1UDI

8

6.2

9

32

8.04

34

19

6.4

16

1VFB

-

-

-

22

8.52

65

150

8.7

22

1WEJ

-

-

-

81

8.36

42

156

9.82

18

1WQ1

125

7.1

10

610

9.9

5

32

9.79

11

2BTF

-

-

-

553

6.39

3

-

-

-

2JEL

164

6

3

45

4.49

86

66

6.81

35

2MTA

136

9

4

-

-

-

4

7.57

48

2QFW

-

-

-

-

-

-

68

9.01

11

2SIC

57

8.8

8

173

8.62

18

127

4.59

6

2SNI

256

9.6

7

534

9.69

4

-

-

-

7CEI

61

8.7

5

106

7.11

28

-

-

-

Summary

  

HEX

 

ZDOCK

 

LZerD

 

Mean

 

206

 

173

 

164

 

Rank<100

 

17

 

19

 

22

 

Rank<500

 

32

 

33

 

34

 

Rank<1000

 

42

 

39

 

38

 

Rank<2000

 

43

 

41

 

47

 

Win

 

18

 

20

 

22

 
  1. The results of HEX are taken from the columns of "U-U shape-only Blind search" in Table 3 of the paper by Ritchie et al. (2008). ZDOCK results are taken from the decoy set downloaded. Among the 84 test cases, complexes for which none of the three methods produced a hit i.e. ligand RMSD (lRMSD) less than 10 Ã… are excluded from the table. In this table the ligand RMSD is used to indicate the quality of predictions to be consistent with the HEX docking results. Cases where either docking algorithm obtains a better rank are highlighted in bold. "-" indicates that the algorithm was unable to find a hit among the top 2000 predictions. Mean in summary shows the MLR score (Eqn. 16).
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BMC Bioinformatics

ISSN: 1471-2105

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