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Table 2 Evaluation and comparison of the performances of Pep-3D-Search.

From: Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis

PDB ID 1jrh 1bj1 1g9m 1e6j 1n8z 1iqd 1yy9 2adf 1avz 1hx1 Average
CED ID CE0179 CE0175 CE0058 CE0170 CE0096 CE0176 CE0199 CE0154 -- --  
Epitope size 21 19 15 11 20 16 15 15 16 24  
Antigen size 94 93 304 209 580 155 612 188 102 111  
Pep-3D-Search
TP/PE 19/40 7/13* 10/39 11/36 20/35* 6/47 10/25 12/36 10/39 13/39  
MCC 0.3902 0.1442 0.1394 0.2285 0.1856 0.0356 0.1030 0.2153 0.1643 0.152 0.1758
Sensitivity 0.475 0.5833 0.2564 0.3056 0.5714 0.1277 0.4 0.3333 0.2564 0.3333 0.3642
Precision 0.9048 0.3684 0.6667 1.0 1.0 0.375 0.6667 0.8 0.625 0.5417 0.6948
PepSurf
TP/PE 19/28 2/17 9/31 10/30 6/11 8/31 1/8* 10/18 14/25 12/25  
MCC 0.4134 -0.0537 0.1257 0.2056 0.0596 0.1272 0.0067 0.1832 0.3348 0.1863 0.1589
Sensitivity 0.6786 0.1176 0.2903 0.3333 0.5455 0.2581 0.125 0.5556 0.56 0.48 0.3944
Precision 0.9048 0.1053 0.6 0.9091 0.3 0.5 0.0476 0.6667 0.875 0.5 0.5409
Mapitope
TP/PE 19/22 2/18 13/33 1/6 9/13 15/106 3/23* 0/10 6/9* 5/21  
MCC 0.4224 -0.062 0.1899 0.0154 0.0909 0.2401 0.0209 -0.0173 0.1387 0.0135 0.1053
Sensitivity 0.8636 0.1111 0.3939 0.1667 0.6923 0.1415 0.1304 0.0 0.6667 0.2381 0.3404
Precision 0.9048 0.1053 0.8667 0.0909 0.45 0.9375 0.1429 0.0 0.375 0.2083 0.4081
  1. TP: number of true positives; PE: number of residues in the predicted epitope; TN: number of true negatives; FP: number of false positives; FN: number of false negatives; Matthews correlation coefficient ( MCC ) = ( T P T N ) ( F P F N ) ( T P + F P ) ( T P + T N ) ( T N + F P ) ( T N + F N ) MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaeiikaGIaeeyta0Kaee4qamKaee4qamKaeiykaKIaeyypa0tcfa4aaSaaaeaacqGGOaakcqWGubavcqWGqbaucqGHflY1cqWGubavcqWGobGtcqGGPaqkcqGHsislcqGGOaakcqWGgbGrcqWGqbaucqGHflY1cqWGgbGrcqWGobGtcqGGPaqkaeaadaGcaaqaaiabcIcaOiabdsfaujabdcfaqjabgUcaRiabdAeagjabdcfaqjabcMcaPiabcIcaOiabdsfaujabdcfaqjabgUcaRiabdsfaujabd6eaojabcMcaPiabcIcaOiabdsfaujabd6eaojabgUcaRiabdAeagjabdcfaqjabcMcaPiabcIcaOiabdsfaujabd6eaojabgUcaRiabdAeagjabd6eaojabcMcaPaqabaaaaaaa@613F@ ; Sensitivity  ( Se ) = T P T P + F N MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaee4uamLaeeyzauMaeeOBa4Maee4CamNaeeyAaKMaeeiDaqNaeeyAaKMaeeODayNaeeyAaKMaeeiDaqNaeeyEaKNaeeiiaaIaeiikaGIaee4uamLaeeyzauMaeiykaKIaeyypa0tcfa4aaSaaaeaacqWGubavcqWGqbauaeaacqWGubavcqWGqbaucqGHRaWkcqWGgbGrcqWGobGtaaaaaa@4963@ ; Precision  ( Pr ) = T P T P + F P MathType@MTEF@5@5@+=feaagaart1ev2aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaeeiuaaLaeeOCaiNaeeyzauMaee4yamMaeeyAaKMaee4CamNaeeyAaKMaee4Ba8MaeeOBa4MaeeiiaaIaeiikaGIaeeiuaaLaeeOCaiNaeiykaKIaeyypa0tcfa4aaSaaaeaacqWGubavcqWGqbauaeaacqWGubavcqWGqbaucqGHRaWkcqWGgbGrcqWGqbauaaaaaa@466F@ .
  2. *For the cases, the best prediction was found in the second-ranked candidate.