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Table 5 Comparison of the predictive performance of Pep-3D-Search with different distance parameters (AHA).

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

PDB ID 1jrh 1bj1 1g9m 1e6j 1n8z 1iqds 1yy9 2adf 1avz 1hx1 Average
AHA (distance threshold = 3.7)
TP/PE 17/20 7/16 12/44 11/34 17/36* 6/32 6/25* 9/33 13/36 8/32  
MCC 0.375 0.1243 0.1716 0.2286 0.1565 0.0733 0.0595 0.1502 0.2855 0.0351 0.1659
Sensitivity 0.85 0.4375 0.2727 0.3235 0.4722 0.1875 0.24 0.2727 0.3611 0.25 0.3667
Precision 0.8095 0.3684 0.8 1.0 0.85 0.375 0.4 0.6 0.8125 0.3333 0.6349
AHA (distance threshold = 4)
TP/PE 16/20 7/10 13/42 8/30 15/30* 5/39 6/23 10/37 12/35 10/34  
MCC 0.3491 0.1528 0.1887 0.1584 0.1379 0.0283 0.0598 0.1695 0.2525 0.0858 0.1583
Sensitivity 0.8 0.7 0.3095 0.2667 0.5 0.1282 0.2609 0.2703 0.3429 0.2941 0.3873
Precision 0.7619 0.3684 0.8667 0.7273 0.75 0.3125 0.4 0.6667 0.75 0.4167 0.6021
AHA (distance threshold = 4.3)
TP/PE 16/18 8/11 14/42 8/36 17/30* 9/37 4/16* 11/37 10/33 4/26  
MCC 0.3537 0.1773 0.2052 0.1558 0.1571 0.1431 0.0394 0.1923 0.1869 -0.0514 0.1559
Sensitivity 0.8889 0.7273 0.3333 0.2222 0.5667 0.2432 0.25 0.2973 0.303 0.1538 0.3986
Precision 0.7619 0.4211 0.9333 0.7273 0.85 0.5625 0.2667 0.7333 0.625 0.1667 0.6048
AHA (distance threshold = 4.6)
TP/PE 19/36 9/24 9/44 4/41 18/38 0/34 8/25* 8/36* 5/37 6/27  
MCC 0.3989 0.1483 0.1206 0.0495 0.1663 -0.1023 0.0813 0.1241 -0.0357 0.0051 0.0956
Sensitivity 0.5278 0.375 0.2045 0.0976 0.4737 0.0 0.32 0.2222 0.1351 0.2222 0.2578
Precision 0.9048 0.4737 0.6 0.3636 0.9 0.0 0.5333 0.5333 0.3125 0.25 0.4871
  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.