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Table 3 The lowest lRMSD to each of the known crystal structures for AdK is calculated over all paths that reach the goal within 3.5Ã….

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

PDB id

lowest lRMSD (Ã…)

 

1ake → 4ake

4ake → 1ake

1e4v

0.32

3.17

1e4y

0.93

3.02

2eck

0.35

3.17

1ank

0.48

3.13

1zin

2.24

2.76

1zio

3.75

3.19

1zip

2.09

2.79

1s3g

1.71

3.31

1p3j

1.48

3.37

2eu8

1.31

3.04

2p3s

1.47

3.30

2oo7

1.26

3.06

2ori

1.30

3.04

2osb

1.31

3.07

2rh5

3.82

2.82

2rgx

2.93

3.34

1aky

1.44

3.12

2aky

1.30

3.30

3aky

1.41

3.14

1dvr

2.91

3.02

1zak

2.81

3.99

2ar7

3.65

3.10

2bbw

3.79

3.38

2c9y

3.17

3.73

1ak2

2.94

4.04

2ak2

2.89

3.97

2ak3

3.78

3.73

  1. The value shown in column 2 is the minimum lowest lRMSD obtained over the best run (in terms of depth) of the method using the COMBINE90−10 global bias scheme over the progress coordinate, no local bias for the expansion procedure, and the reactive temperature scheme for the 1ake to 4ake transition. Column 3 shows the minimum lowest lRMSD for the 4ake to 1ake transition. Column 1 shows the PDB id of each of the crystal structures considered. The structures are ordered according to their locations along the 1ake to 4ake transition.
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BMC Structural Biology

ISSN: 1472-6807

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