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Table 4 Ranking ZDOCK2.3 decoys (IRMSD ≤4Å) by the jackknife test

From: Designing coarse grained-and atom based-potentials for protein-protein docking

Complexa

Rankb

 

ADPs-II c

Zdock2.3

DARS

ACE

1AK4

-

-

950

1744

1B6C

95

16

9

178

1BVK

12

268

610

-

1DQJ

-

1490

-

-

1EWY

164

18

42

364

1FC2

484

-

24

797

1GHQ

-

-

-

1308

1HIA

21

653

122

-

1IJK

1131

-

368

-

1KLU

-

-

-

-

1AVX

5

46

6

59

1D6R

1840

567

-

-

1E96

39

399

42

490

1F34

13

26

666

5

1GCQ

1030

-

1057

1040

1GRN

210

102

-

-

1I4D

84

403

965

616

1KXP

91

7

1

200

1NSN

53

445

-

-

1SBB

-

-

-

-

1ACB

113

55

24

98

1AKJ

592

40

-

-

1AY7

120

100

-

-

1DFJ

37

1

-

-

1EAW

65

13

33

309

1FQ1

-

-

-

-

1GP2

4

389

58

1681

1I9R

184

14

589

-

1UDI

27

13

1

1

2PCC

203

193

821

120

1AHW

23

14

-

-

1BUH

14

-

555

-

1E6E

2

103

44

520

1ML0

10

1

9

32

1PPE

3

1

1

1

1QFW

544

74

-

-

1TMQ

9

126

12

22

1WEJ

3

42

1047

-

2JEL

307

86

76

579

7CEI

15

1

920

708

1ATN

-

-

-

-

1BJ1

6

18

18

85

1CGI

71

247

13

24

1F51

1

11

251

797

1KAC

121

1389

-

-

1KKL

283

-

1

222

1NCA

4

4

-

-

1QA9

687

-

-

-

2SNI

17

618

1

2

1RLB

48

302

5

7

  1. a-Complex PDB code.
  2. b-Rank of the lowest energy near-native decoy with IRMSD ≤4Å out of 54000 predictions.
  3. c-Jackknife test (see Methods)
  4. -- No near-native decoy identified among the 2000 best ranked decoys.
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BMC Structural Biology

ISSN: 1472-6807

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