Skip to main content

Table 2 Quality measures of trained classifiers and comparison with publicly available caspase cut site prediction models.

From: Pripper: prediction of caspase cleavage sites from whole proteomes

Classifier ACC PRC FDR SPC MCC
SVM-6-4 87,4% 85,3% 14,7% 84,4% 74,8%
RF-12-12 85,7% 82,5% 17,5% 82,5% 71,7%
J48-4-2 81,6% 79,7% 20,3% 78,3% 63,3%
Vote 96,8% 100% 0,0% 100% 93,7%
PeptideCutter 50,8% 63,0% 37,0% 97,7% 4,6%
GraBCas 67,7% 67,6% 32,4% 67,5% 35,4%
CASVM P4-P1 62,3% 83,0% 17% 93,7% 31,6%
CASVM P4-P2' 72,7% 73,1% 26,9% 73,6% 45,4%
CASVMP14-P10' 83,1% 81,6% 18,4% 80,1% 66,2%
  1. Peptide cutter, GraBCas and CASVM were all tested with the complete training data. The values obtained from SVM-6-4, J48-4-2 and RF-12-12 represent the values obtained from the test sequences of the training with the leave-one-out method. The default cut off value 1.2 was used in GraBCas. Classifiers RF-12-12 and SVM-6-4 were used in the Vote classifier. Abbreviations: ACC, accuracy; PRC, precision; FDR, false discovery rate; SPC, specificity; MCC, Matthews correlation coefficient.