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Table 3 Comparison of ML-Select and MUFOLD-CL

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

# M ML-Select MUFOLD-CL
   B1 B 1−2 B 1−3 B1 B 1−2 B 1−3
1dtdb n 11.2% 11.3% 11.7% 56.2% 71.6% 76.6%
  p 100% 100% 100% 2.42% 2.34% 2.36%
  s 0.26% 0.26% 0.3% 54.3% 71.2% 75.7%
1wapa n 0.31% 0.6% 0.8% 39.4% 55.1% 60.6%
  p 100% 100% 100% 0.51% 0.49% 0.49%
  s 0.002% 0.003% 0.004% 39% 56.4% 61.8%
1hz6a n 4.6% 4.6% 4.6% 43.1% 48.5% 60.6%
  p 99.8% 99.4% 98.5% 9.3% 9.2% 9.5%
  s 0.44% 0.44% 0.45% 44.2% 50.5% 60.6%
1tig n 3.7% 6.2% 7.1% 46.1% 61% 66.8%
  p 100% 100% 100% 2.1% 2.2% 2.2%
  s 0.08% 0.14% 0.16% 49.4% 61.3% 67.3%
1dtja n 7.5% 7.9% 8.6% 57.3% 82.1% 83.5%
  p 100% 100% 99.6% 3.0% 3.3% 3.3%
  s 0.23% 0.25% 0.27% 59.8% 78.7% 79.3%
1bq9 n 0.62% 1.4% 2.4% 38.1% 47.7% 61.4%
  p 100% 95.1% 83% 0.19% 0.2% 0.23%
  s 0.002% 0.004% 0.01% 57.8% 68.9% 76.6%
1ail n 1.4% 3.8% 3.8% 44.2% 62.3% 63.8%
  p 100% 92.5% 86% 0.48% 0.53% 0.53%
  s 0.01% 0.023% 0.025% 50.9% 65.3% 66.9%
1c8ca n 0.8% 1.0% 1.1% 46.7% 59% 64.6%
  p 100% 99% 89.1% 2.37% 2.4% 2.41%
  s 0.02% 0.03% 0.034% 54.8% 68.4% 74.7%
2ci2 n 0% 0% 0% 45.3% 64.5% 71.7%
  p 0% 0% 0% 3.3% 3.4% 3.4%
  s 0.01% 0.02% 0.03% 45.3% 61.9% 69%
1fwp n 1.84% 4.5% 4.5% 61.3% 68% 72%
  p 97.7% 75.4% 60.3% 0.17% 0.16% 0.16%
  s 0.003% 0.008% 0.01% 53.6% 61% 66%
1sap n 2.63% 2.63% 2.63% 45.7% 48.9% 52.6%
  p 87.8% 71.7% 70.6% 6.0% 5.9% 6.0%
  s 0.21% 0.25% 0.26% 53.4% 58% 62%
1hhp n 12.2% 18.3% 24.2% 61.2% 65.3% 85.7%
  p 84.2% 74.8% 68% 0.09% 0.08% 0.09%
  s 0.012% 0.02% 0.03% 57.8% 67.5% 77.1%
2ezk n 1.3% 1.3% 1.3% 58.4% 69.5% 78.4%
  p 59.3% 45.6% 40.3% 1.57% 1.57% 1.6%
  s 0.03% 0.045% 0.51% 59.5% 70.6% 78.3%
1aoy n 0.11% 0.23% 0.29% 57.3% 75% 79.7%
  p 92.4% 92.1% 86.8% 25.8% 25.9% 25.8%
  s 0.03% 0.07% 0.09% 57% 74.2% 79.2%
2h5nd n 6.8% 6.8% 6.8% 43.6% 52.7% 60.5%
  p 94.1% 83.4% 71.4% 0.35% 0.36% The 0.37%
  s 0.028% 0.029% 0.034% 50.7% 59.3% 66.4%
1isua n 0.021% 0.043% 0.064% 57.4% 69.3% 72.3%
  p 17.5% 16.8% 16.4% 7.8% 7.7% 7.7%
  s 0.01% 0.02% 0.03% 56.8% 69.4% 72.6%
1cc5 n 0.16% 0.16% 0.16% 58.8% 69.9% 72.8%
  p 50% 42.7% 36.5% 7.3% 7.31% 7.3%
  s 0.022% 0.026% 0.03% 54.3% 64.5% 67.2%
1aly n 4.12% 5.2% 6.2% 47.9% 54.1% 63.9%
  p 42.6% 42% 41.7% 0.35% 0.33% 0.34%
  s 0.035% 0.044% 0.054% 50.5% 60.2% 69.7%
  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