Table 2 Analysis of conformations obtained by the branch-and-pruning algorithm on the three proteins targets: 2JMY, 2KXA and 2KSL

Number of

residues

15

15

15

24

51

Number of

vertices

107

107

107

170

359

Definition

of α helices

1-15

3-13

5-11

1-11, 13-23

4-11, 13-27,

29-36, 41-50

Position

tolerance (Å)

0.2

0.2

0.2

0.2

0.2

Angle

tolerance (°)

2

2

2

4

4

b value

4

4

4

8

4

Number of

long-range

constraints

0

0

0

1

3

Number of saved

conformations

1

10000

10000

10000

10000

Number of generated

conformations

1

633,937

928,399

3,380,964

491,498

CPU time

-

1 min

1 min

25 min

31 min

Number of violated

constraints (> 1Å)

0

4.0 ± 2.1

11.6 ± 3.6

9.6 ± 2.9

12.8 ± 1.1

Maximum

violation (Å)

0

3.3 ± 1.4

4.8 ± 0.7

3.7 ± 1.0

8.1 ± 0.6

Mininum RMSD

from PDB structure (Å)

1.4

1.3

2.1

1.1

3.0

RMSD from PDB structure

for minimum violated

conformations (Å)

1.4

2.9

2.8

1.3

3.5

PROCHECK

core residues (%)

100

65.7 ± 25.9

49.2 ± 7.6

60.4 ± 8.1

76.9 ± 2.4

allowed residues (%)

0

17.9 ± 9.7

40.9 ± 8.3

39.6 ± 8.0

21.3 ± 2.8

gen.allow. residues (%)

0

3.6 ± 4.8

9.9 ± 7.2

0.0 ± 0.0

1.9 ± 1.7

disall. residues (%)

0

0.0 ± 0.0

0.0 ± 0.0

0.0 ± 0.0

0.0 ± 0.0