Skip to main content

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