Skip to main content

Table 2 Docking success rate S 1 1 (in %) of ML SFs trained on Pr and tested on Cr complexes when characterized by different features.

From: Machine-learning scoring functions for identifying native poses of ligands docked to known and novel proteins

Y (T) Model Feature set
   X A R G XA XR XG AR AG RG XAR XAG XRG ARG XARG Average
BA (1105) MARS 28.72 20.00 5.13 18.46 34.36 36.92 28.21 21.03 16.41 8.21 37.95 28.72 40.00 8.21 36.41 24.58
  RF 23.08 23.08 10.77 24.10 30.52 30.77 37.44 21.54 30.00 25.65 31.03 34.12 39.75 25.90 32.31 28.00
  SVM 26.67 30.26 4.62 19.49 30.77 23.08 29.23 20.51 41.54 30.26 26.15 42.05 37.44 38.97 41.54 29.51
  MLR 43.08 18.97 9.74 28.21 33.33 46.67 47.18 21.03 40.00 33.85 46.15 49.23 49.74 40.00 51.28 37.23
  BRT 23.85 25.39 9.24 39.23 30.52 30.26 42.31 22.82 37.69 33.85 33.85 44.36 44.62 36.67 43.08 33.18
  kNN 17.95 11.28 8.72 16.41 9.23 18.46 15.90 11.28 15.38 17.95 15.38 17.44 21.03 14.36 17.44 15.21
  Average 27.22 21.50 8.04 24.32 28.12 31.03 33.38 19.71 30.17 24.96 31.75 35.99 38.76 27.35 37.01 27.95
RMSD (1105) MARS 45.64 42.05 26.15 72.31 54.87 52.31 73.85 33.85 70.26 71.28 52.82 70.26 72.82 67.18 75.90 58.77
  RF 32.72 32.31 13.85 67.39 39.80 42.26 70.36 32.10 64.82 68.10 41.95 64.82 72.00 64.51 67.18 51.61
  SVM 29.74 28.72 6.15 66.15 37.95 30.77 70.77 32.31 61.54 56.41 45.64 64.10 62.05 58.97 63.08 47.62
  MLR 44.62 35.90 6.15 70.26 58.46 54.36 72.31 40.51 70.26 65.64 56.92 75.90 70.26 67.69 69.23 57.23
  BRT 38.77 34.87 8.10 70.98 52.00 41.13 74.77 35.59 67.70 69.02 48.92 71.39 72.51 65.33 67.49 54.57
  kNN 31.79 24.10 3.08 55.38 30.77 17.44 62.56 15.90 40.00 38.97 22.05 44.62 45.13 37.95 41.03 34.05
  Average 37.21 32.99 10.58 67.08 45.64 39.71 70.77 31.71 62.43 61.57 44.72 65.18 65.79 60.27 63.98 50.64
RMSD (1105x50) MARS 44.10 31.79 5.13 72.82 62.56 49.74 75.38 34.87 73.33 70.77 64.10 76.92 72.31 72.31 78.97 59.01
  RF 39.39 48.10 22.46 70.77 61.95 54.77 72.41 50.97 73.64 75.18 63.79 76.00 75.49 75.28 76.90 62.47
  SVM 36.41 43.08 10.26 66.15 54.87 43.08 70.77 43.08 71.79 65.13 57.95 74.36 72.31 69.74 70.77 56.65
  MLR 45.64 36.41 6.15 70.26 56.92 52.31 73.34 37.95 71.79 71.28 57.44 72.82 71.79 70.77 73.33 57.88
  BRT 46.15 36.92 13.33 71.59 54.36 54.87 71.59 42.56 70.77 70.77 56.92 70.26 72.31 71.28 71.28 58.33
  kNN 36.41 46.15 23.59 61.03 51.28 41.03 71.28 45.13 60.00 53.33 49.23 61.54 60.51 53.33 55.90 51.32
  Average 41.35 40.41 13.49 68.77 57.01 49.30 72.46 42.43 70.22 67.69 58.24 72.05 70.68 69.23 70.63 57.61