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Table 4 Comparison of the predictive performance of Pep-3D-Search with different distance parameters (CA).

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
CA (distance threshold = 6.5)
TP/PE 5/5 2/10 13/42 10/43 18/36* 7/31 2/10* 0/20 12/31 13/31  
MCC 0.1119 -0.0014 0.1887 0.2033 0.1664 0.1015 0.019 -0.0367 0.262 0.1889 0.1204
Sensitivity 1.0 0.2 0.3095 0.2326 0.5 0.2258 0.2 0.0 0.3871 0.4194 0.3474
Precision 0.2381 0.1053 0.8667 0.9091 0.9 0.4375 0.1333 0.0 0.75 0.5417 0.4882
CA (distance threshold = 7)
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
CA (distance threshold = 7.5)
TP/PE 19/38 12/27* 10/45 9/33 18/40 0/36 7/25 12/36 9/37 9/36  
MCC 0.3947 0.2349 0.1374 0.1812 0.1662 -0.0895 0.0704 0.2153 0.1332 0.0411 0.1485
Sensitivity 0.5 0.4444 0.2222 0.2727 0.45 0.0 0.28 0.3333 0.2432 0.25 0.2996
Precision 0.9048 0.6316 0.6667 0.8182 0.9 0.0 0.4667 0.8 0.5625 0.375 0.6126
CA (distance threshold = 8)
TP/PE 20/39 12/28* 10/40 10/35 17/36 0/37 5/26 13/35 8/39 5/32  
MCC 0.4248 0.2309 0.1391 0.2047 0.1565 -0.1144 0.0484 0.2378 0.0822 -0.065 0.1345
Sensitivity 0.5128 0.4286 0.25 0.2857 0.4722 0.0 0.1923 0.3714 0.2051 0.1563 0.2874
Precision 0.9524 0.6316 0.6667 0.9091 0.85 0.0 0.3333 0.8667 0.5 0.2083 0.5918
  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.