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Table 2 Comparison of the five basin-selection strategies

From: Decoy selection for protein structure prediction via extreme gradient boosting and ranking

#

M

ML-Select

Basin-Size

Basin-Size+Energy

PR

PR+PC

  

B1

B 1−2

B 1−3

B1

B 1−2

B 1−3

B1

B 1−2

B 1−3

B1

B 1−2

B 1−3

B1

B 1−2

B 1−3

1dtdb

n

11.2%

11.3%

11.7%

88.3%

92.4%

92.4%

88.3%

92.4%

92.4%

0%

0%

0%

4.1%

5.1%

93.4%

 

p

100%

100%

100%

99.6%

99.6%

99.9%

99.6%

99.6%

97.2%

0%

0%

0%

100%

100%

93.4%

 

s

0.26%

0.26%

0.3%

2.1%

2.2%

2.2%

2.1%

2.2%

2.2%

0.002%

0.009%

0.01%

0.09%

0.12%

2.2%

1wapa

n

0.31%

0.6%

0.8%

83.7%

83.7%

83.7%

83.7%

83.7%

83.7%

0%

0%

2.3%

0%

0%

0%

 

p

100%

100%

100%

99%

87.8%

79.3%

99%

89.4%

81.5%

0%

0%

80%

0%

0%

0%

 

s

0.002%

0.003%

0.004%

0.43%

0.48%

0.5%

0.43%

0.47%

0.5%

0.001%

0.003%

0.02%

0.02%

0.05%

0.08%

1hz6a

n

4.6%

4.6%

4.6%

35.9%

35.9%

44.7%

35.9%

35.9%

35.9%

0.02%

0.02%

0.02%

2.2%

2.6%

4.6%

 

p

99.8%

99.4%

98.5%

99.7%

77.6%

81%

99.7%

92.3%

73%

67.6%

67.1%

66.2%

100%

99.3%

92.2%

 

s

0.44%

0.44%

0.45%

3.4%

4.4%

5.3%

3.4%

3.7%

4.7%

0.25%

0.25%

0.25%

0.21%

0.25%

0.47%

1tig

n

3.7%

6.2%

7.1%

35.2%

42.9%

48%

35.2%

42.9%

48%

0%

0%

0%

2.9%

4.1%

5.6%

 

p

100%

100%

100%

99.6%

99.5%

99.1%

99.6%

99.5%

99.1%

0%

0%

0%

100%

100%

98.7%

 

s

0.08%

0.14%

0.16%

0.8%

0.95%

1.1%

0.8%

0.95%

1.1%

0.002%

0.003%

0.005%

0.06%

0.09%

0.13%

1dtja

n

7.5%

7.9%

8.6%

54.5%

59.4%

62%

54.5%

59.4%

61.4%

0%

0%

0.15%

2.15%

2.84%

4.94%

 

p

100%

100%

99.6%

98.6%

97.3%

97%

98.6%

97.3%

97.3%

0%

0%

60%

100%

93.1%

87%

 

s

0.23%

0.25%

0.27%

1.74%

1.9%

2%

1.74%

1.9%

1.98%

0.002%

0.003%

0.008%

0.07%

0.09%

0.18%

1bq9

n

0.62%

1.4%

2.4%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

 

p

100%

95.1%

83%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

 

s

0.002%

0.004%

0.01%

0.07%

0.12%

0.17%

0.04%

0.1%

0.16%

0.002%

0.02%

0.05%

0.02%

0.04%

0.06%

1ail

n

1.4%

3.8%

3.8%

0%

0%

0%

0%

0%

0.92%

0%

0%

0%

0%

0%

0.3%

 

p

100%

92.5%

86%

0%

0%

0%

0%

0%

3%

0%

0%

0%

0%

0%

1.6%

 

s

0.01%

0.023%

0.025%

0.14%

0.22%

0.3%

0.05%

0.13%

0.17%

0.001%

0.005%

0.008%

0.034%

0.063%

0.11%

1c8ca

n

0.8%

1.0%

1.1%

1.1%

6.2%

8.6%

1.4%

6.5%

7.6%

0.11%

0.11%

0.11%

0.06%

0.11%

1.21%

 

p

100%

99%

89.1%

16.7%

52.1%

52.7%

86.2%

94.4%

56.2%

40%

33.3%

28.6%

5.3%

4.9%

34.9%

 

s

0.02%

0.03%

0.034%

0.18%

0.33%

0.46%

0.044%

0.2%

0.4%

0.009%

0.009%

0.01%

0.03%

0.06%

0.1%

2ci2

n

0%

0%

0%

0%

0%

0%

0.77%

0.77%

0.77%

0.51%

0.51%

0.51%

0%

0%

0.26%

 

p

0%

0%

0%

0%

0%

0%

48.4%

23.4%

15.2%

90.9%

83.3%

76.9%

0%

0%

7.6%

 

s

0.01%

0.02%

0.03%

0.06%

0.12%

0.18%

0.05%

0.1%

0.17%

0.02%

0.02%

0.021%

0.03%

0.07%

0.11%

1fwp

n

1.84%

4.5%

4.5%

0%

0%

0%

0%

0%

0%

9.3%

9.3%

9.3%

0%

1.3%

1.3%

 

p

97.7%

75.4%

60.3%

0%

0%

0%

0%

0%

0%

77.8%

70%

63.6%

0%

3.7%

2.4%

 

s

0.003%

0.008%

0.01%

0.06%

0.12%

0.17%

0.05%

0.1%

0.15%

0.017%

0.019%

0.02%

0.03%

0.05%

0.08%

1sap

n

2.63%

2.63%

2.63%

9.3%

14.8%

20.9%

0%

1.5%

10.8%

0%

0%

0%

0.4%

0.8%

1.6%

 

p

87.8%

71.7%

70.6%

85%

84.6%

88.3%

0%

26.9%

65.4%

0%

0%

0%

100%

86.7%

92.4%

 

s

0.21%

0.25%

0.26%

0.8%

1.2%

1.7%

0.2%

0.4%

1.2%

0.002%

0.003%

0.005%

0.03%

0.07%

0.12%

1hhp

n

12.2%

18.3%

24.2%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

 

p

84.2%

74.8%

68%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

 

s

0.012%

0.02%

0.03%

0.06%

0.13%

0.19%

0.06%

0.1%

0.16%

0.007%

0.03%

0.08%

0.03%

0.06%

0.08%

2ezk

n

1.3%

1.3%

1.3%

0%

0%

0%

1.83%

1.83%

1.83%

0%

0%

0%

0%

0%

0%

 

p

59.3%

45.6%

40.3%

0%

0%

0%

51.6%

19.8%

14%

0%

0%

0%

0%

0%

0%

 

s

0.03%

0.045%

0.51%

0.09%

0.16%

0.23%

0.06%

0.15%

0.21%

0.01%

0.02%

0.03%

0.03%

0.07%

0.11%

1aoy

n

0.11%

0.23%

0.29%

0.12%

0.12%

0.15%

0.03%

0.2%

0.5%

0%

0%

0.08%

0%

0.1%

0.18%

 

p

92.4%

92.1%

86.8%

43.9%

22.8%

19%

10.8%

53.5%

67%

0%

0%

80%

0%

34.1%

47.4%

 

s

0.03%

0.07%

0.09%

0.07%

0.14%

0.2%

0.06%

0.12%

0.18%

0.002%

0.004%

0.03%

0.05%

0.08%

0.1%

2h5nd

n

6.8%

6.8%

6.8%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

 

p

94.1%

83.4%

71.4%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

 

s

0.028%

0.029%

0.034%

0.07%

0.14%

0.2%

0.06%

0.11%

0.17%

0.065%

0.075%

0.077%

0.03%

0.07%

0.09%

1isua

n

0.021%

0.043%

0.064%

0.06%

0.13%

0.56%

0.02%

0.11%

0.11%

0%

0%

0%

0.02%

0.17%

0.17%

 

p

17.5%

16.8%

16.4%

8.1%

8.2%

24.3%

3.4%

8.1%

5.6%

0%

0%

0%

7.1%

29.6%

16.7%

 

s

0.01%

0.02%

0.03%

0.062%

0.12%

0.18%

0.05%

0.1%

0.15%

0.003%

0.013%

0.015%

0.023%

0.045%

0.08%

1cc5

n

0.16%

0.16%

0.16%

0%

0.03%

0.08%

0.6%

0.65%

0.97%

0%

0%

0%

0%

0%

0%

 

p

50%

42.7%

36.5%

0%

1.6%

3.1%

59.5%

33.8%

34.3%

0%

0%

0%

0%

0%

0%

 

s

0.022%

0.026%

0.03%

0.05%

0.11%

0.17%

0.07%

0.13%

0.19%

0.005%

0.007%

0.01%

0.035%

0.06%

0.09%

1aly

n

4.12%

5.2%

6.2%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

 

p

42.6%

42%

41.7%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

0%

 

s

0.035%

0.044%

0.054%

0.056%

0.11%

0.17%

0.051%

0.11%

0.16%

0.01%

0.024%

0.026%

0.025%

0.055%

0.081%

  1. The top G1−x groups of decoys selected from each selection strategy, with x limited to 3, are analyzed. When analyzing B1−x, the top x basins are merged. The analysis lists the metrics (M): percentage of near-native decoys (n); the purity (p), which is the proportion of near-native decoys relative to the size of a group; and the relative size (s, is proportional to |Ω|) of each basin
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