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Table 3 Comparison for the Benchmark 2.0 unbound complexes.

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

 

Original ZDOCK Rank

Context Shapes (CS)

PatchDock

ZDOCK Decoys Reranked by LZerD Score

LZerD

Complex

Rank a)

iRMSD

HIT2K

Rank

iRMSD

RMSD

iRMSD

Rank

iRMSD

HIT2K

Rank

iRMSD

HIT2K

1AHW

268

2.28

21

402

2.46

181

2.49

15

1.68

50

5

1.34

42

1AK4

-b)

-

-

-

-

-

-

(NA

NA

NA)

43787

2.35

0

1AKJ

4872

2.29

0

-

-

-

-

1985

1.93

1

-

-

-

1AVX

2863

2.23

0

-

-

-

-

5689

2.22

0

786

2.41

2

1AY7

5584

1.33

0

-

-

-

-

394

1.1

7

1884

1.98

1

1B6C

1717

2.43

2

-

-

-

-

497

2.13

8

1001

2.41

1

1BJ1

129

0.86

49

1893

1.93

-

-

306

1.01

20

298

1.86

7

1BUH

14556

2.37

0

-

-

-

-

11230

2.42

0

12251

1.6

0

1BVK

3970

1.94

0

-

-

2754

2.27

9560

2.43

0

5515

2.24

0

1BVN

502

1.97

13

34

2.34

-

-

8

2.26

59

27

2.32

6

1CGI

145

2.44

9

-

-

1120

2.11

1775

2.14

1

9041

2.1

0

1D6R

2951

2.03

0

-

-

-

-

5022

2.49

0

2619

2.24

0

1DFJ

9

2.27

40

-

-

-

-

9350

2.14

0

-

-

-

1DQJ

2287

2.48

0

-

-

-

-

5391

2.32

0

20816

2.09

0

1E6E

22643

2.08

0

-

-

-

-

432

1.94

2

52

2.13

8

1E6J

15

1.56

34

-

-

-

-

2509

1.81

0

439

2.18

8

1E96

3094

2.26

0

-

-

-

-

882

1.88

2

216

2.14

2

1EAW

3

1.54

62

94

2.29

85

2.29

5

1.48

111

20

2.42

10

1EWY

259

2.32

2

-

-

-

-

1007

2.14

4

349

2.36

14

1EZU

1100

1.94

3

-

-

-

-

589

1.42

4

824

1.21

2

1F34

5

2.2

13

-

-

490

1.81

5082

1.61

0

-

-

-

1F51

230

2.18

4

-

-

-

-

154

1.76

5

3545

1.58

0

1FQJ

9889

2.29

0

-

-

-

-

628

2.39

2

-

-

-

1FSK

1

1.63

105

20

1.57

221

2.39

29

1.57

76

15

2.4

11

1GCQ

24339

2.29

0

-

-

-

-

39221

2.29

0

9418

1.8

0

1GHQ

-

-

-

-

-

-

-

(NA

NA

NA)

15357

1.68

0

1GRN

1704

2.34

2

-

-

-

-

1884

1.74

1

1407

2.18

1

1HE1

4672

1.31

0

1029

2.17

-

-

51

2

8

267

1.98

2

1HIA

-

-

-

-

-

-

-

(NA

NA

NA)

44189

2.42

0

1I9R

50

2.45

41

-

-

-

-

57

1.96

10

95

2.39

21

1IJK

52731

2.44

0

-

-

-

-

39460

2.44

0

6731

2.45

0

1IQD

612

2.27

5

-

-

-

-

36

0.99

27

41

1.2

18

1JPS

171

1.81

9

-

-

-

-

5305

1.37

0

292

0.9

20

1K4C

20806

1.53

0

-

-

-

-

4468

1.18

0

1188

1.43

7

1KAC

2896

2.33

0

-

-

-

-

1313

2.33

1

655

2.18

3

1KTZ

53599

1.69

0

-

-

-

-

33926

1.69

0

12162

1.19

0

1KXP

1734

2.36

1

-

-

-

-

32023

1.91

0

14208

2.22

0

1KXQ

212

1.91

13

2226

1.73

-

-

629

1.24

4

73

1.68

14

1MAH

92

1.31

9

597

1.16

887

2.28

541

0.89

6

92

0.87

2

1ML0

36

1.56

21

-

-

231

2.02

406

1.37

6

559

2.38

3

1MLC

110

1.19

12

18

2.28

-

-

243

1.07

12

1834

1.16

1

1NCA

14

1.93

47

-

-

-

-

302

1.55

12

12528

1.5

0

1NSN

185

1.81

5

26

1.79

-

-

147

1.81

13

945

2.29

1

1PPE

1

0.57

218

2

2.31

-

-

1

0.72

194

1

0.83

68

1QA9

5672

1.88

0

-

-

-

-

5924

1.82

0

1381

2.19

3

1QFW

257

1.14

7

597

1.73

-

-

136

2.31

17

108

1.24

4

1RLB

-

-

-

-

-

-

-

(NA

NA

NA)

46073

1.24

0

1TMQ

314

1.88

11

783

1.68

1

1.96

90

1.45

19

50

1.45

5

1UDI

258

2.17

4

2649

2.14

27

2.42

219

2.39

3

59

2.36

6

1VFB

2734

1.79

0

228

2.46

-

-

1534

1.61

1

1303

1.69

1

1WEJ

465

2.37

8

-

-

-

-

916

1.97

1

3914

2.06

6

1WQ1

1101

2.49

2

-

-

-

-

284

2.05

2

141

1.87

2

2JEL

45

1.79

33

-

-

-

-

149

2.44

19

133

2.49

9

2MTA

-

-

-

-

-

515

2.19

(NA

NA

NA)

606

1.64

11

2PCC

-

-

-

-

-

-

-

(NA

NA

NA)

4542

2.31

0

2QFW

832

2.29

3

33

2.32

-

-

42

1.99

17

68

1.55

29

2SIC

173

1.86

24

1077

2.28

-

-

17

1.85

61

12

2.04

9

2SNI

17906

2.44

0

-

-

-

-

428

2.33

2

-

-

-

7CEI

106

1.97

24

2290

1.9

366

1.07

705

1.57

7

6765

2.03

0

Summary c)

  

ZDOCK

CS

PatchDock (PD)

LZerD Rerank

LZerD

Rank<100

11

7

3

11

14

Rank<500

26

9

6

26

23

Rank<1000

29

12

9

32

29

Rank<2000

33

15

10

38

36

Wins vs. LZerD Rerank

ZDOCK/LZerD Rerank

26/26

CS/LZerD Rerank

5/34

PD/LZerD Rerank

7/34

-

-

Wins vs. LZerD

ZDOCK/LZerD

24/33

CS/LZerD

5/34

PD/LZerD

8/34

LZerD Rerank/LZerD

24/28

-

  1. LZerD results are compared with ZDOCK, Context Shapes, and PatchDock. ZDOCK results are based on the decoy structures downloaded from the ZDOCK benchmark website. Among the 84 unbound complexes in the ZDOCK Benchmark 2.0, 60 complexes are included in this table. The rest of the 23 complexes are not included as neither ZDOCK nor LZerD produced any hits within the top 54000 predictions. Another complex (2VIS) has also been excluded as LZerD needed more memory than our computer could provide. Data for Context Shapes and PatchDock are taken from the previously published paper of the Context Shapes (Table 4 in the paper by Shentu et al.). The number of hits within top 2000 (HIT2K) are not provided for Context Shapes and PatchDock because the data are not shown in their paper. Also note that hits ranked over 3600 are not provided by their paper.
  2. a) "-" indicates that the algorithm was unable to find a hit among the top 54000 predictions. "NA" in the block "Reranked by LZerD score" indicates that no hits were found in the ZDOCK decoy set analyzed.
  3. b) The Ranks column shows the best rank of hits (predictions with an interface RMSD of less than 2.5 Ã…). iRMSD shows the interface RMSD of the best ranked hit. HITS2K is the number of hits found in the top 2000 ranked predictions.
  4. c) Summary shows the number of cases where the best rank below 100, 500, 1000, and 2000 are obtained. Wins vs. LZerD indicates the number of cases in which either the algorithm or LZerD has a better rank. In comparison with Context Shapes and PatchDock, hits above the rank 3600 are not considered for LZerD since hits over 3600 are not provided for Context Shapes and PatchDock in the paper by Shentu et al.