Skip to main content

Table 2 Average (μ) and standard deviations (σ) are reported for the lowest tree lRMSD over 10 executions of the method.

From: Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method

System

Start → Goal

μ ± σ over lowest lRMSDs (Å)

  

QUAD+LB

LINEAR+LB

UNIFORM+LB

COMBINE 90-10 +LB

Trp-Cage (20 aa)

E → 1l2y (18 Å)

1.86 ± 0.53

2.12 ± 0.57

1.83 ± 0.63

1.87 ± 0.43

CaM (140 aa)

1cfd → 1cll (10.7 Å)

1cll → 1cfd (10.7 Å)

3.17 ± 0.25

3.35 ± 0.51

3.27 ± 0.10

3.56 ± 0.29

3.49 ± 0.26

3.70 ± 0.23

3.32 ± 0.12

3.50 ± 0.21

 

1cfd → 2f3y (9.9 Å)

2f3y → 1cfd (9.9 Å)

3.93 ± 0.37

3.43 ± 0.39

3.93 ± 0.42

3.65 ± 0.45

3.99 ± 0.24

3.62 ± 0.13

3.76 ± 0.41

3.34 ± 0.13

 

1cll → 2f3y (13.44 Å)

2f3y → 1cll (13.44 Å)

1.91 ± 0.58

0.82 ± 0.30

1.67 ± 0.49

0.72 ± 0.08

2.01 ± 0.86

1.02 ± 0.43

1.68 ± 0.37

0.73 ± 0.10

AdK (214 aa)

1ake → 4ake (6.95 Å)

4ake → 1ake (6.95 Å)

3.91 ± 0.34

4.65 ± 0.71

4.28 ± 0.36

5.32 ± 0.79

5.15 ± 0.30

5.62 ± 0.37

4.19 ± 0.22

5.21 ± 0.41

  1. Weighting schemes for global bias over node selection are compared here. Local bias is incorporated in the expansion procedure.
Back to article page

BMC Structural Biology

ISSN: 1472-6807

Contact us