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Table 1 Prediction performance of selected representative servers at two scenarios: a) thresholds that correctly predict ~80% of T-cell epitopes; b) thresholds that correctly predict ~50% of T-cell epitopes.

From: Evaluation of MHC-II peptide binding prediction servers: applications for vaccine research

Server Threshold TP FN TN FP TP (tumor epitopes)
a) 80% prediction
IEDB_ARB 100 10 5 56 32 17 (81%)
IEDB_ CON 11 10 5 70 18 17 (81%)
MHCPRED 15 10 5 36 52 17 (81%)
MULTI_ANN 3 15 0 38 50 17 (81%)
MULTI_SVM 6.4 13 2 59 29 17 (81%)
NETMHCII 4000 12 3 51 37 17 (81%)
NETMHCIIPAN 440 12 3 56 32 17 (81%)
PROPRED -1.5 14 1 54 34 17 (81%)
RANKPEP 0.85 12 3 41 47 17 (81%)
b) 50% prediction
IEDB_ARB 3 7 8 80 8 10 (48%)
IEDB_ CON 4 7 8 86 2 10 (48%)
MHCPRED 3 4 11 76 12 10 (48%)
MULTI_ANN 5 5 10 66 22 11 (52%)
MULTI_SVM 7.1 6 9 82 6 10 (48%)
NETMHCII 400 7 8 78 10 10 (48%)
NETMHCIIPAN 60 7 8 87 1 10 (48%)
PROPRED 0 10 5 81 7 11 (52%)
RANKPEP 7 10 5 69 19 11 (52%)