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Table 3 The optimized weights of energy terms calculated by BARS for protein 1ctfA (after 6 iterations), 1iloA (after 5 iterations), 1iieA (after 5 iterations)

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

Energy terms

Initial weights

Final weights

Final weights

Final weights

  

for 1ctfA

for 1iloA

for 1iieA

Env

1.00

1.30

1.98

5.69

Pair

1.00

2.59

2.02

1.09

Vdw

1.00

0.55

0.72

0.20

Hs

1.00

0.09

0.82

1.28

Ss

1.00

0.48

0.37

0.20

Sheet

1.00

3.48

1.90

1.14

R-sigma

1.00

0.53

1.11

0.19

Cb

1.00

0.05

0.24

1.62

Rg

3.00

0.49

2.63

0.31

Co

1.00

0.00

0.00

0.62

Ramachandran

0.00

1.02

0.43

0.27

Hb-srbb

0.00

2.41

0.80

0.36

Hb-lrbb

0.00

0.00

0.00

0.00

  1. The Manhattan distance of the weights of 1ctfA and 1iieA is 15.56, and that between 1ctfA and 1iloA is 12.39, while that between 1iloA and 1iieA is only 8.95. The cosine values of weight vectors are 0.63, 0.47, 0.77, respectively