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Table 2 Results & Runtime

From: Computing H/D-Exchange rates of single residues from data of proteolytic fragments

 

Instance

    

Improved-ILP

Lagrange

Heuristic

Name

n

P

n / P

ℱ

ϵ

T 1

T all

# -Sol

T 1

T all

T 1

Cabin

78

26

3.0

34

128

0.02

3.25

36

1.36

8.35

0.02

CytoC

74

18

4.1

17

40

0.03

0.37

1980

0.27

6.10

0.01

   Subproblem 1

27

5

5.4

6

6

0.01

0.01

1

0.01

0.01

0.003

   Subproblem 2

26

5

5.2

6

30

0.01

0.32

110

0.17

5.81

0.004

   Subproblem 3

15

6

2.5

5

4

0.01

0.04

18

0.09

0.28

0.004

FKBP V1 (ilp)

101

34

3.0

31

47

0.04

1.18

37800

1.03

137.36

0.017

   Subproblem 1

35

15

2.3

12

15

0.01

0.45

126

0.57

32.83

0.009

   Subproblem 2

16

5

3.2

5

4

0.01

0.02

4

0.04

0.05

0.003

   Subproblem 3

36

12

3.0

14

28

0.02

0.71

75

0.42

104.48

0.005

FKBP V2 (mem)

101

34

3.0

31

46

0.03

13.82

1160040

2.03

560.56

0.02

   Subproblem 1

35

15

2.3

12

16

0.01

4.41

840

1.26

305.4

0.007

   Subproblem 2

16

5

3.2

5

2

0.01

0.01

1

0.01

0.01

0.002

   Subproblem 3

36

12

3.0

14

28

0.01

9.4

1381

0.76

255.15

0.007

FKBP V3 (xiii)

103

34

3.0

47

38

0.05

0.16

6

0.14

0.13

0.026

   Subproblem 1

22

10

2.2

16

12

0.01

0.04

1

0.02

0.03

0.008

   Subproblem 2

10

4

2.5

4

2

0.01

0.02

3

0.02

0.02

0.002

   Subproblem 3

11

5

2.2

4

0

0.01

0.01

1

0.02

0.01

0.003

   Subproblem 4

25

10

2.5

22

24

0.01

0.08

2

0.07

0.06

0.008

   Subproblem 5

3

1

3.0

1

0

0.01

0.01

1

0.01

0.01

0.001

FKBP V4 (both)

105

43

2.4

56

58

0.05

0.96

1536

0.88

7.15

0.032

   Subproblem 1

49

20

2.5

24

18

0.02

0.55

24

0.8

6.08

0.012

   Subproblem 2

11

5

2.2

4

0

0.01

0.01

2

0.02

0.01

0.003

   Subproblem 3

25

12

2.1

26

40

0.01

0.39

16

0.5

1.05

0.009

   Subproblem 4

4

3

1.3

2

0

0.01

0.01

2

0.01

0.01

0.002

Myoglobin

152

49

3.1

48

42

0.1

0.98

1121760

1.13

13.25

0.023

   Subproblem 1

17

9

1.9

10

14

0.02

0.16

20

0.22

1.98

0.004

   Subproblem 2

12

2

6.0

4

2

0.01

0.01

2

0.01

0.01

0.002

   Subproblem 3

22

8

2.8

8

8

0.01

0.26

82

0.34

8.56

0.005

   Subproblem 4

37

14

2.6

17

14

0.01

0.49

38

0.45

2.51

0.009

   Subproblem 5

3

1

3.0

1

0

0.01

0.01

1

0.01

0.01

0.002

   Subproblem 6

21

6

3.5

6

4

0.02

0.03

9

0.08

0.16

0.003

   Subproblem 7

4

1

4.0

1

0

0.01

0.01

1

0.01

0.01

0.001

   Subproblem 8

7

1

7.0

1

0

0.01

0.01

1

0.01

0.01

0.002

  1. We give the characteristics of the instance, i.e., the number of residues (n), the number of fragments (|ℱ|), the number of non-equivalent parts (|P|), the average length of these parts (n/|P|) and the minimal error of an solution (ϵ). We give the solution times in seconds to compute one (T1) and all (T all ) solutions and the number of solutions found (#-Sol) all with respect to the improved-ILP. Furthermore we give the running times for our Lagrangian approach and the error and running time of the heuristic.
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BMC Bioinformatics

ISSN: 1471-2105

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