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Table 1 Overall performance of ElliPro in comparison with other methods#.

From: ElliPro: a new structure-based tool for the prediction of antibody epitopes

  ElliPro (radius 6Å) PPI-PRED PatchDock ClusPro (DOT)   
  Best prediction (score 0.5) Average (score 0.5) 1st prediction (score 0.7) ProMate (patch) 1st patch best patch 1st model best model of top 10 1st model best model of top 10 CEP (average) DiscoTope (-7.7)
Overall statistics
sensitivity 0.601 0.165 0.093 0.091 0.153 0.331 0.300 0.425 0.258 0.453 0.310 0.416
1-specificity 0.138 0.109 0.047 0.083 0.161 0.135 0.135 0.114 0.079 0.067 0.223 0.214
precision 0.291 0.119 0.158 0.101 0.083 0.188 0.175 0.262 0.235 0.390 0.110 0.155
accuracy 0.840 0.832 0.879 0.841 0.780 0.819 0.816 0.846 0.863 0.892 0.739 0.754
AUC 0.732 0.528 0.523 0.504 0.496 0.598 0.583 0.656 0.589 0.693 0.544 0.601
P-value 0.00E+00 1.37E-04 9.52E-06 2.74E-01 1.0E+00 7.8E-30 9.0E-23 0.0E+00 7.9E-34 0.0E+00 4.3E-06 4.1E-25
Statistics averaged over epitopes
sensitivity 0.58 ± 0.25 0.17 ± 0.10 0.10 ± 0.20 0.09 ± 0.17 0.15 ± 0.24 0.34 ± 0.32 0.29 ± 0.26 0.42 ± 0.29 0.25 ± 0.31 0.46 ± 0.28 0.34 ± 0.28 0.43 ± 0.31
1-specificity 0.12 ± 0.10 0.11 ± 0.04 0.05 ± 0.03 0.08 ± 0.03 0.16 ± 0.07 0.14 ± 0.07 0.15 ± 0.06 0.13 ± 0.07 0.10 ± 0.07 0.08 ± 0.05 0.28 ± 0.20 0.22 ± 0.15
precision 0.44 ± 0.22 0.13 ± 0.06 0.16 ± 0.28 0.11 ± 0.20 0.10 ± 0.17 0.21 ± 0.24 0.19 ± 0.20 0.30 ± 0.25 0.25 ± 0.33 0.41 ± 0.29 0.11 ± 0.08 0.18 ± 0.12
accuracy 0.85 ± 0.08 0.82 ± 0.05 0.87 ± 0.05 0.83 ± 0.05 0.77 ± 0.07 0.81 ± 0.08 0.80 ± 0.08 0.83 ± 0.09 0.84 ± 0.09 0.88 ± 0.07 0.69 ± 0.17 0.74 ± 0.12
AUC 0.73 ± 0.11 0.53 ± 0.03 0.53 ± 0.10 0.51 ± 0.09 0.50 ± 0.13 0.60 ± 0.17 0.57 ± 0.14 0.64 ± 0.17 0.58 ± 0.17 0.69 ± 0.15 0.53 ± 0.08 0.60 ± 0.13
  1. # – best prediction, patch, or model corresponds to the most significant (minimal P-value) of the predicted epitopes