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Table 4 Comparative evaluation of recent predictors

From: Algorithmic approaches to protein-protein interaction site prediction

PredName Year Label Dataset Precision Recall Accuracy AUC MCC F1 Source
ProMate 2004 A DB3-188 36.5 30.3 77.1 67.7 19.5 33.1 [34]
   B DS56B 31.9 27.3 76.7 63.3 15.6 29.4  
   C DS56U 28.7 27.3 76.6 62.7 14.0 28.0  
   E NI2 40.0 93.9 13.6 56.1 [37]
   F PlaneDimers 68.0 18.0 [33]
   G TransComp_1 70.0 20.0  
ConsPPISP 2005 A DB3-188 46.5 30.6 80.4 73.2 26.7 36.9 [34]
   B DS56B 39.8 36.1 78.9 72.6 25.2 37.9  
   C DS56U 37.4 34.5 79.5 71.2 23.8 35.9  
   E NI2 49.3 32.2 14.7 39.0 [37]
PINUP 2006 A DB3-188 40.7 34.7 78.3 66.0 24.6 37.5 [34]
   B DS56B 37.3 31.9 78.4 63.7 21.7 34.4  
   C DS56U 30.4 30.1 76.9 60.0 16.4 30.2  
   E NI2 52.9 28.5 15.1 37.0 [37]
WHISCY 2006 H W025 39.0 27.0 27.0 [40]
metaPPISP 2007 A DB3-188 49.0 26.7 81.1 74.6 26.2 34.6 [34]
   B DS56B 43.3 25.8 80.8 74.4 22.9 32.3  
   C DS56U 38.9 24.0 81.1 71.5 20.2 29.7  
   E NI2 54.7 25.5 16.6 34.8 [37]
   F PlaneDimers 54.0 4.0 [33]
   G TransComp_1 78.0 31.0  
PIER 2007 E NI2 44.1 83.6 23.0 57.7 [37]
SPPIDER 2007 J S149 63.7 60.3 76.0 42.0 [40]
   F PlaneDimers 80.0 33.0 [33]
   G TransComp_1 68.0 15.0  
Sikic 2009 L 3DS 63.4 78.3 65.3 30.8 [38]
PredUs 2010 A DB3-188 43.6 45.7 [31]
   B DS56B 41.5 42.2  
   C DS56U 39.8 44.6  
  2011 A DB3-188 50.3 57.5 72.6 73.9 34.5 53.0 [32]
   B DS56B 43.0 53.0 72.1 71.3 29.0 47.4  
   C DS56U 43.3 53.6 73.2 72.9 30.4 47.9  
   K S58 45.5 57.6 78.5 37.7 50.8 [7]
VORFFIP 2011 J S149 63.4 74.7 90.0 58.0 [40]
   H W025 42.0 47.0 38.0  
   M B100 45.0 56.0 42.0 49.0  
HomPPI 2011 N BM180 1 58.0 85.0 44.0 [20]
    BM180 2 48.0 84.0 42.0  
    BM180 3 71.0 86.0 60.0  
    BM180 4 73.0 91.0 65.0  
PrISE 2012 A DB3-188 48.0 43.2 80.6 77.2 33.8 45.5 [34]
   B DS56B 46.1 45.4 80.9 77.6 34.1 45.7  
   C DS56U 43.7 44.0 81.2 75.5 32.6 43.8  
Li mRMR-IFS 2012 L 3DS 65.3 79.0 67.3 34.8 [38]
Chen PDM-ML 2012 I S435 51.2 66.2 75.9 42.0 57.8 [7]
   J S149 § 51.9 67.7 75.3 42.3 58.8  
   K S58 44.6 65.4 77.7 40.3 53.0  
PresCont 2012 F PlaneDimers 80.0 33.0 [33]
   G TransComp_1 69.0 17.0  
RAD-T 2014 A DB3-188 28.5 64.7 65.2 22.2 35.5 [37]
   D NI1 33.8 80.5 51.8 20.1 46.4  
   E NI2 44.7 80.9 59.1 26.4 57.6  
  1. refers to the DB3-188 set excluding 2VIS; refers to the S435 set excluding 3 proteins due to obsolescence or absence; §refers to the S149 set excluding 7 proteins due to existence in training set. BM180 1 are transient enzyme-inhibitor complexes, BM180 2 are transient non-enzyme- inhibitor complexes, BM180 3 are obligate hetero-dimers and BM180 1 are obligate homo-dimers.