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Table 2 Conservation threshold analysis.

From: HopDock: a probabilistic search algorithm for decoy sampling in protein-protein docking

PDB ID

Threshold

Nr. Triangles

lRMSD (Å)

Rrest - Rinterface

1FLT (V,Y)

0.25

2417

2.06

6.67

 

0.50

2338

1.12

-3.50

 

0.75

2080

1.03

1.27

1WWW (W, Y)

0.25

2900

2.29

-18.37

 

0.50

2911

2.24

-7.45

 

0.75

2854

2.60

6.62

1C1Y (A,B)

0.25

3385

1.89

-13.65

 

0.50

3325

1.30

-38.64

 

0.75

3306

1.45

-21.01

  1. Table shows the effect of three different conservation thresholds 0.25, 0.5, and 0.75 on the number of active triangles and lowest lRMSD to native structure.
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