Skip to main content

Table 6 Cutoff distances (nm), binding constants (molecule −1 s −1), unbinding rate constants (s −1), and σ values for the rule-based model for various resolutions of the native, S-shaped, and U-shaped Pen a 1

From: Extending rule-based methods to model molecular geometry and 3D model resolution

  

Model percent reduction

Cfg

Value

0 %

25 %

50 %

65 %

75 %

90 %

95 %

N

Cutoff

7.0–8.7

5.6–6.2

5.5

5.5

4.0–5.4

4.0–5.4

4.0–5.4

 

k f1

1.00

1.00

1.00

1.00

1.00

1.00

1.00

 

k f2

6.60e–03

7.58e–03

3.86e–03

4.90e–04

1.27e–03

1.17e–02

1.64e–02

 

k r

0.01

0.01

0.01

0.01

0.01

0.01

0.01

 

σ

7.03e–04

3.62e–04

6.30e–05

1.62e–03

6.31e–04

1.29e–04

9.25e–04

S

Cutoff

6.8–8.3

5.8–6.0

5.8–6.0

5.8–6.0

5.4–5.7

4.5–5.3

4.5–5.3

 

k f1

1.00

1.00

1.00

1.00

1.00

1.00

1.00

 

k f2

3.56e–03

1.03e–02

8.67e–03

7.84e–03

4.12e–03

6.38e–03

5.58e–03

 

k r

0.01

0.01

0.01

0.01

0.01

0.01

0.01

 

σ

1.35e–04

1.65e–03

1.48e–04

3.78e–04

9.40e–05

6.77e–04

4.00e–05

U

Cutoff

6.8-8.6

6.8–8.6

5.3

5.3

5.3

4.1–5.2

3.9–4.0

 

k f1

1.00

1.00

1.00

1.00

1.00

1.00

1.00

 

k f2

7.32e-03

1.07e–02

1.94e–03

1.18e–03

1.01e–02

1.04e–02

4.26e–03

 

k r

0.01

0.01

0.01

0.01

0.01

0.01

0.01

 

σ

4.69e–04

1.41e–03

5.97e–04

2.77e–04

5.23e–04

3.18e–04

2.59e–04