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Table 1 Comparison of CO with MolLoc.

From: A global optimization algorithm for protein surface alignment

  

CO

MolLoc

Rank

Protein Pair

N. corresp atoms

RMSD

SAS

N. corresp atoms

RMSD

SAS

1

atpE-1hck

62

1.2

1.94

45

1.3

2.89

2

1atpE-1phk

57

0.91

1.6

63

0.9

1.43

3

1atpE-1csn

50

1.18

2.36

55

0.9

1.64

4

1atpE-1nsf

34

2.11

6.21

11

1.4

12.73

5

1atpE-1j7k

25

1.81

7.24

25

1.6

6.4

6

1atpE-1e8xA

24

1.74

7.25

20

1.7

8.5

7

1atpE-1f9aC

21

2.17

10.33

18

1.6

8.89

8

1atpE-1kay

20

1.9

9.5

8

1.7

21.25

9

1atpE-1yag

20

1.92

9.6

17

1.6

9.41

10

1atpE-1a82

19

2.02

10.63

13

1.9

14.62

11

1atpE-1jjv

18

1.76

9.78

10

1.8

18

12

1atpE-1gn8A

17

2.37

13.94

14

1.6

11.43

13

1atpE-1b8aA

16

2.05

12.81

10

2

20

14

1atpE-1mjhA

16

2.28

14.25

14

1.9

13.57

15

1atpE-1e2q

15

1.39

9.27

5

1.8

36

16

1atpE-1kp2A

13

1.51

11.62

15

1.9

12.67

17

1atpE-1ayl

12

1.21

10.08

16

2

12.5

18

1atpE-1g5t

7

2.26

32.29

8

1.6

20

   

avg.SAS

10.04

 

avg.SAS

12.88

  1. Pairwise comparisons of the binding site of protein 1atp with other 18 proteins all binding ATP (columns 2). The results of CO (columns 3-5) and MolLoc (columns 6-8). For a de_nition of SAS see the text. The comparisons are ranked based on the number of corresponding atoms in CO (column 3).
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BMC Bioinformatics

ISSN: 1471-2105

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