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Table 2 Weights of energy terms during the iteration process of BARS

From: Constructing effective energy functions for protein structure prediction through broadening attraction-basin and reverse Monte Carlo sampling

  

Weights at iteration

Energy terms

Initial weights

#1

#2

#3

#4

#5

#6

Env

1.00

1.00

0.97

0.48

0.49

1.26

1.30

Pair

1.00

1.23

1.22

0.64

2.71

2.62

2.59

Vdw

1.00

1.06

0.88

0.61

0.55

0.55

0.55

Hs

1.00

1.70

1.70

1.06

0.09

0.09

0.09

Ss

1.00

1.00

1.00

0.48

0.48

0.48

0.48

Sheet

1.00

1.00

1.00

1.00

3.48

3.48

3.48

R-sigma

1.00

1.00

1.00

0.53

0.53

0.53

0.53

Cb

1.00

0.02

0.01

0.41

0.00

0.00

0.05

Rg

3.00

3.00

3.14

6.05

0.49

0.49

0.49

Contact order

1.00

1.00

1.05

0.74

0.00

0.00

0.00

Ramachandran

0.00

0.00

0.00

0.01

0.91

1.01

1.02

Hb-srbb

0.00

0.00

0.02

0.00

3.27

2.49

2.41

Hb-lrbb

0.00

0.00

0.00

0.00

0.00

0.00

0.00

  1. Here, the initial weights were set as the weights used by Rosetta in score3. A total of 6 iterations are shown here. The Manhattan distances of each adjacent weighting are 1.97, 0.44, 6.62, 17.47, 1.74, 0.21, respectively. The iteration process stopped when the Manhattan distance is less than a threshold of 0.3. The cosine of angle of weight vectors at iterations #4 and #5 is 0.98, while that of iterations #5 and #6 reaches 0.99