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Table 13 The Docking Results of DoBi, ZDOCK and 3D-Dock on CAPRI

From: Protein-protein binding site identification by enumerating the configurations

Target DoBi1000 ZDOCK DoBi10 3D-Docke
  iRMSDa NCb F l c F r d iRMSD NC F l F r iRMSD NC F l F r iRMSD NC
T1 4.28 27.6 56.0 45.2 8.10 17.2 50.0 32.0 5.45 44.0 74.1 64.3 3.0 46
T2 6.23 76.9 38.8 35.3 4.15 46.2 51.9 35.7 8.27 53.8 48.0 36.4
T3 18.48 9.4 17.1 43.9 3.89 62.5 64.0 60.6 18.51 12.0 22.9 51.4
T4 3.98 63.5 66.6 57.1 4.50 23.1 78.2 58.3 6.24 35.9 38.3 51.6 15.1 21
T5 11.06 7.7 46.8 31.6 10.08 5.4 76.6 18.9 11.06 7.7 46.8 31.6
T6 16.49 15.4 36.4 33.4 8.72 29.2 54.2 71.6 19.21 9.6 18.2 28.1 0.8 86
T7 11.10 13.5 62.8 24.0 6.43 2.7 44.4 4.8 11.10 13.5 62.8 24.0 28.6 14
T8 6.69 37.9 42.7 60.9 2.73 63.6 82.8 60.0 6.69 37.9 42.7 60.9 1.7 33
T9 2.85 33.3 61.3 67.6 8.46 28.9 54.1 58.7 10.54 1.4 36.7 37.7 9.7 23
T10 4.52 28.9 50.4 51.8 14.75 5.9 15.4 17.3 7.69 13.0 58.1 59.3 34.8 0
T11 2.55 66.7 68.5 75.0 2.63 61.1 96.0 82.1 12.17 0 0 45.0 1.9 20
T12 2.55 66.7 68.5 75.0 2.31 81.5 75.9 88.9 12.17 0 0 45.0 3.2 22
T13 3.33 94.1 74.1 69.6 2.49 57.1 52.9 59.3 3.33 94.1 74.1 69.6 6.4 6
T14 19.98 9.6 34.5 28.0 5.22 42.0 72.7 68.9 20.97 10.3 36.1 28.3 0.9 47
T15 2.40 53.6 86.9 83.0 0.86 91.1 90.6 81.8 4.00 42.0 64.2 63.6
T18 8.08 25.0 57.7 44.4 1.88 66.2 80.0 80.0 11.38 8.2 10.3 19.7 9.4 14
T19 2.74 58.8 60.0 69.0 9.81 4.8 40.0 14.6 2.74 58.8 60.0 69.0 3.9 31
T20 15.13 1.1 14.7 28.6 13.62 7.2 35.0 37.1 15.13 1.1 14.7 28.6
T21 2.02 50.0 77.8 68.8 2.43 70.7 83.3 70.6 2.02 50.0 77.8 68.8
T22 16.08 7.5 20.0 71.4 9.28 12.6 66.7 0 16.08 7.5 20.0 71.4
T23 1.90 61.2 86.9 88.4 2.14 72.1 87.3 87.9 3.14 46.0 83.1 83.1
T24 5.01 50.0 31.6 20.0 28.15 0 0 0 5.01 50.0 31.6 20.0
T26 7.11 29.6 26.1 45.2 30.07 0 0 0 7.11 29.6 26.1 45.2
T27 6.95 60.0 42.4 51.9 15.89 3.5 24.4 0 7.38 66.7 38.5 50.0
T29 2.46 68.6 83.3 79.3 3.90 58.6 77.4 72.1 3.80 32.7 69.4 77.8
  1. aC α iRMSD between the configuration by the respective method and the experimental structure.
  2. bNC (%) is fraction of native contacts for each method.
  3. cF l (%) is the F-score of each method for the ligand protein on the data set.
  4. dF r (%) is the F-score of each method for the receptor protein on the data set.
  5. eThe values for 3D-Dock are from literatures [36, 37]; The blank results mean that 3D-Dock never produced on these targets.