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Table 1 Summary of predictions using different population sizes and clustering thresholds

From: Effect of conformation sampling strategies in genetic algorithm for multiple protein docking

  

No Pairwise Clusters

5Ã… Pairwise Clusters

10Ã… Pairwise Clusters

PDB

Population Size

RMSD (Ã…)1

fnat2

Rank

RMSD (Ã…)1

fnat2

Rank

RMSD (Ã…)1

fnat2

Rank

1ES7

200

17.51

0.03

20

17.94

0.03

16

1.86

0.92

3

 

400

9.85

0.25

159

7.95

0.63

47

1.86

0.92

3

 

600

14.21

0.00

445

9.56

0.34

265

1.86

0.92

3

 

800

2.15

0.70

18

7.23

0.64

2

1.86

0.92

3

1K2X

200

18.52

0.00

84

21.20

0.01

61

6.05

0.49

74

 

400

20.36

0.01

239

6.05

0.49

80

23.69

0.01

195

 

600

6.14

0.46

250

2.12

0.51

1

23.41

0.01

599

 

800

19.45

0.01

56

19.26

0.02

718

6.04

0.49

60

1WWW

200

19.16

0.02

51

13.49

0.11

152

8.62

0.58

23

 

400

5.34

0.52

10

15.58

0.00

115

2.48

0.78

12

 

600

17.37

0.03

248

15.76

0.03

182

11.12

0.39

13

 

800

16.30

0.00

160

17.19

0.02

615

2.48

0.78

14

  1. GA runs were carried out for 1000 generations. The crossover operation was not used.
  2. 1The Global C-α RMSD between the best prediction in the final population and the native structure, for each simulation.
  3. 2fnat is the fraction of correctly predicted interface residues.
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BMC Proceedings

ISSN: 1753-6561

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