Table 6

Performances of different computational approaches for predicting AMP functional activities based on balanced independent test datasets

ActivityMethodPrecisionSensitivitySpecificityAccuracyF1MCCAUC
AntibacterialAMAP0.57880.87500.36330.61920.69670.27740.6192
AMPDiscover-RF0.61620.88030.45180.66600.72500.36750.6322
AMPDiscover-RNN0.61320.87270.44950.66110.72030.35570.6611
iAMP-CA2L0.49900.68260.31480.49870.5766-0.00280.4987
iAMPCN0.67090.79140.61180.70160.72620.40990.7621
AntifungalAMAP0.53540.82280.28600.55440.64870.12890.5544
AMPDiscover-RF0.53850.78510.32720.55610.63880.12630.5398
AMPDiscover-RNN0.53160.78950.30440.54690.63540.10730.5469
AMPfun0.59010.57460.60090.58770.58220.17550.6256
dbAMP0.55240.80440.34820.57630.65500.17150.6082
iAMP-CA2L0.50000.21400.78600.50000.29980.00000.5000
iAMP-RAAC0.58500.67630.52020.59820.62730.19890.5982
iAMPCN0.73470.53680.80610.67150.62040.35610.7483
AntiviralAMAP0.30420.23360.46560.34960.2643-0.30920.3496
AMPDiscover-RF0.42830.54320.27490.40910.4790-0.18880.4999
AMPDiscover-RNN0.44470.56830.29020.42930.4989-0.14730.4293
AMPfun0.58620.75020.47050.61030.65820.22990.6653
dbAMP0.53920.86180.26350.56270.66330.15640.6006
iAMP-CA2L0.46150.02430.97170.49800.0461-0.01260.4980
iAMP-RAAC0.61560.66530.58450.62490.63950.25060.6249
iAMPCN0.82480.73080.84480.78780.77500.57940.8865
AnticancerAMAP0.39730.41180.37530.39350.4044-0.21300.3935
AMPfun0.44500.41720.47960.44840.4306-0.10340.4444
dbAMP0.48280.63440.32040.47740.5483-0.04760.4759
iAMP-RAAC0.46580.11720.86560.49140.1873-0.02590.4914
iAMPCN0.68300.76670.64410.70540.72240.41390.7698
Anti-Gram positiveAMPfun0.56070.88650.30540.59600.68690.23590.6304
dbAMP0.55130.82650.32720.57680.66140.17740.6107
iAMP-RAAC0.55900.88790.29950.59370.68600.23170.5937
iAMPCN0.63720.79950.54490.67220.70920.35610.7246
Anti-Gram negativeAMPfun0.56830.88680.32620.60650.69270.25720.6390
dbAMP0.56030.85150.33170.59160.67580.21440.6232
iAMP-RAAC0.56350.85820.33540.59680.68030.22710.5968
iAMPCN0.63350.80580.53380.66980.70930.35290.7212
Anti-mammalian cellsAMPfun0.60240.35740.76410.56080.44860.13300.6163
dbAMP0.53740.64860.44160.54510.58780.09230.5585
iAMP-RAAC0.63640.17690.89890.53790.27680.10960.5379
iAMPCN0.67480.79420.61730.70580.72970.41810.7665
Anti-HIVAMAP0.38790.28300.55350.41820.3273-0.16990.4182
iAMP-CA2L0.33330.00630.98740.49690.0123-0.03250.4969
iAMPCN0.84890.74210.86790.80500.79190.61490.8633
Anti-MRSAiAMP-CA2L0.95650.41510.98110.69810.57890.48060.6981
iAMPCN0.86000.81130.86790.83960.83500.68030.8597
AntiparasiticAMAP0.26920.16090.56320.36210.2014-0.30130.3621
AMPDiscover-RF0.50000.72410.27590.50000.59150.00000.6092
AMPDiscover-RNN0.48410.70110.25290.47700.5728-0.05140.4770
AMPfun0.47500.43680.51720.47700.4551-0.04610.4970
iAMP-CA2L0.40000.02300.96550.49430.0435-0.03440.4943
iAMP-RAAC0.55170.18390.85060.51720.27590.04630.5172
iAMPCN0.75340.63220.79310.71260.68750.43090.7861
AntibiofilmAMAP0.59650.45950.68920.57430.51910.15270.5743
iAMP-CA2L0.85710.08110.98650.53380.14810.15920.5338
iAMPCN0.82430.82430.82430.82430.82430.64860.8667
ChemotacticAMAP0.40000.14290.78570.46430.2105-0.09330.4643
iAMP-CA2L0.00000.00001.00000.50000.00000.00000.5000
iAMPCN1.00000.50001.00000.75000.66670.57740.8163
EndotoxiniAMP-CA2L0.91670.68750.93750.81250.78570.64550.8125
iAMPCN0.70590.75000.68750.71880.72730.43840.7617
InsecticidalAMAP0.55880.22890.81930.52410.32480.05970.5241
iAMPCN0.85140.75900.86750.81330.80250.63020.8936
ActivityMethodPrecisionSensitivitySpecificityAccuracyF1MCCAUC
AntibacterialAMAP0.57880.87500.36330.61920.69670.27740.6192
AMPDiscover-RF0.61620.88030.45180.66600.72500.36750.6322
AMPDiscover-RNN0.61320.87270.44950.66110.72030.35570.6611
iAMP-CA2L0.49900.68260.31480.49870.5766-0.00280.4987
iAMPCN0.67090.79140.61180.70160.72620.40990.7621
AntifungalAMAP0.53540.82280.28600.55440.64870.12890.5544
AMPDiscover-RF0.53850.78510.32720.55610.63880.12630.5398
AMPDiscover-RNN0.53160.78950.30440.54690.63540.10730.5469
AMPfun0.59010.57460.60090.58770.58220.17550.6256
dbAMP0.55240.80440.34820.57630.65500.17150.6082
iAMP-CA2L0.50000.21400.78600.50000.29980.00000.5000
iAMP-RAAC0.58500.67630.52020.59820.62730.19890.5982
iAMPCN0.73470.53680.80610.67150.62040.35610.7483
AntiviralAMAP0.30420.23360.46560.34960.2643-0.30920.3496
AMPDiscover-RF0.42830.54320.27490.40910.4790-0.18880.4999
AMPDiscover-RNN0.44470.56830.29020.42930.4989-0.14730.4293
AMPfun0.58620.75020.47050.61030.65820.22990.6653
dbAMP0.53920.86180.26350.56270.66330.15640.6006
iAMP-CA2L0.46150.02430.97170.49800.0461-0.01260.4980
iAMP-RAAC0.61560.66530.58450.62490.63950.25060.6249
iAMPCN0.82480.73080.84480.78780.77500.57940.8865
AnticancerAMAP0.39730.41180.37530.39350.4044-0.21300.3935
AMPfun0.44500.41720.47960.44840.4306-0.10340.4444
dbAMP0.48280.63440.32040.47740.5483-0.04760.4759
iAMP-RAAC0.46580.11720.86560.49140.1873-0.02590.4914
iAMPCN0.68300.76670.64410.70540.72240.41390.7698
Anti-Gram positiveAMPfun0.56070.88650.30540.59600.68690.23590.6304
dbAMP0.55130.82650.32720.57680.66140.17740.6107
iAMP-RAAC0.55900.88790.29950.59370.68600.23170.5937
iAMPCN0.63720.79950.54490.67220.70920.35610.7246
Anti-Gram negativeAMPfun0.56830.88680.32620.60650.69270.25720.6390
dbAMP0.56030.85150.33170.59160.67580.21440.6232
iAMP-RAAC0.56350.85820.33540.59680.68030.22710.5968
iAMPCN0.63350.80580.53380.66980.70930.35290.7212
Anti-mammalian cellsAMPfun0.60240.35740.76410.56080.44860.13300.6163
dbAMP0.53740.64860.44160.54510.58780.09230.5585
iAMP-RAAC0.63640.17690.89890.53790.27680.10960.5379
iAMPCN0.67480.79420.61730.70580.72970.41810.7665
Anti-HIVAMAP0.38790.28300.55350.41820.3273-0.16990.4182
iAMP-CA2L0.33330.00630.98740.49690.0123-0.03250.4969
iAMPCN0.84890.74210.86790.80500.79190.61490.8633
Anti-MRSAiAMP-CA2L0.95650.41510.98110.69810.57890.48060.6981
iAMPCN0.86000.81130.86790.83960.83500.68030.8597
AntiparasiticAMAP0.26920.16090.56320.36210.2014-0.30130.3621
AMPDiscover-RF0.50000.72410.27590.50000.59150.00000.6092
AMPDiscover-RNN0.48410.70110.25290.47700.5728-0.05140.4770
AMPfun0.47500.43680.51720.47700.4551-0.04610.4970
iAMP-CA2L0.40000.02300.96550.49430.0435-0.03440.4943
iAMP-RAAC0.55170.18390.85060.51720.27590.04630.5172
iAMPCN0.75340.63220.79310.71260.68750.43090.7861
AntibiofilmAMAP0.59650.45950.68920.57430.51910.15270.5743
iAMP-CA2L0.85710.08110.98650.53380.14810.15920.5338
iAMPCN0.82430.82430.82430.82430.82430.64860.8667
ChemotacticAMAP0.40000.14290.78570.46430.2105-0.09330.4643
iAMP-CA2L0.00000.00001.00000.50000.00000.00000.5000
iAMPCN1.00000.50001.00000.75000.66670.57740.8163
EndotoxiniAMP-CA2L0.91670.68750.93750.81250.78570.64550.8125
iAMPCN0.70590.75000.68750.71880.72730.43840.7617
InsecticidalAMAP0.55880.22890.81930.52410.32480.05970.5241
iAMPCN0.85140.75900.86750.81330.80250.63020.8936
Table 6

Performances of different computational approaches for predicting AMP functional activities based on balanced independent test datasets

ActivityMethodPrecisionSensitivitySpecificityAccuracyF1MCCAUC
AntibacterialAMAP0.57880.87500.36330.61920.69670.27740.6192
AMPDiscover-RF0.61620.88030.45180.66600.72500.36750.6322
AMPDiscover-RNN0.61320.87270.44950.66110.72030.35570.6611
iAMP-CA2L0.49900.68260.31480.49870.5766-0.00280.4987
iAMPCN0.67090.79140.61180.70160.72620.40990.7621
AntifungalAMAP0.53540.82280.28600.55440.64870.12890.5544
AMPDiscover-RF0.53850.78510.32720.55610.63880.12630.5398
AMPDiscover-RNN0.53160.78950.30440.54690.63540.10730.5469
AMPfun0.59010.57460.60090.58770.58220.17550.6256
dbAMP0.55240.80440.34820.57630.65500.17150.6082
iAMP-CA2L0.50000.21400.78600.50000.29980.00000.5000
iAMP-RAAC0.58500.67630.52020.59820.62730.19890.5982
iAMPCN0.73470.53680.80610.67150.62040.35610.7483
AntiviralAMAP0.30420.23360.46560.34960.2643-0.30920.3496
AMPDiscover-RF0.42830.54320.27490.40910.4790-0.18880.4999
AMPDiscover-RNN0.44470.56830.29020.42930.4989-0.14730.4293
AMPfun0.58620.75020.47050.61030.65820.22990.6653
dbAMP0.53920.86180.26350.56270.66330.15640.6006
iAMP-CA2L0.46150.02430.97170.49800.0461-0.01260.4980
iAMP-RAAC0.61560.66530.58450.62490.63950.25060.6249
iAMPCN0.82480.73080.84480.78780.77500.57940.8865
AnticancerAMAP0.39730.41180.37530.39350.4044-0.21300.3935
AMPfun0.44500.41720.47960.44840.4306-0.10340.4444
dbAMP0.48280.63440.32040.47740.5483-0.04760.4759
iAMP-RAAC0.46580.11720.86560.49140.1873-0.02590.4914
iAMPCN0.68300.76670.64410.70540.72240.41390.7698
Anti-Gram positiveAMPfun0.56070.88650.30540.59600.68690.23590.6304
dbAMP0.55130.82650.32720.57680.66140.17740.6107
iAMP-RAAC0.55900.88790.29950.59370.68600.23170.5937
iAMPCN0.63720.79950.54490.67220.70920.35610.7246
Anti-Gram negativeAMPfun0.56830.88680.32620.60650.69270.25720.6390
dbAMP0.56030.85150.33170.59160.67580.21440.6232
iAMP-RAAC0.56350.85820.33540.59680.68030.22710.5968
iAMPCN0.63350.80580.53380.66980.70930.35290.7212
Anti-mammalian cellsAMPfun0.60240.35740.76410.56080.44860.13300.6163
dbAMP0.53740.64860.44160.54510.58780.09230.5585
iAMP-RAAC0.63640.17690.89890.53790.27680.10960.5379
iAMPCN0.67480.79420.61730.70580.72970.41810.7665
Anti-HIVAMAP0.38790.28300.55350.41820.3273-0.16990.4182
iAMP-CA2L0.33330.00630.98740.49690.0123-0.03250.4969
iAMPCN0.84890.74210.86790.80500.79190.61490.8633
Anti-MRSAiAMP-CA2L0.95650.41510.98110.69810.57890.48060.6981
iAMPCN0.86000.81130.86790.83960.83500.68030.8597
AntiparasiticAMAP0.26920.16090.56320.36210.2014-0.30130.3621
AMPDiscover-RF0.50000.72410.27590.50000.59150.00000.6092
AMPDiscover-RNN0.48410.70110.25290.47700.5728-0.05140.4770
AMPfun0.47500.43680.51720.47700.4551-0.04610.4970
iAMP-CA2L0.40000.02300.96550.49430.0435-0.03440.4943
iAMP-RAAC0.55170.18390.85060.51720.27590.04630.5172
iAMPCN0.75340.63220.79310.71260.68750.43090.7861
AntibiofilmAMAP0.59650.45950.68920.57430.51910.15270.5743
iAMP-CA2L0.85710.08110.98650.53380.14810.15920.5338
iAMPCN0.82430.82430.82430.82430.82430.64860.8667
ChemotacticAMAP0.40000.14290.78570.46430.2105-0.09330.4643
iAMP-CA2L0.00000.00001.00000.50000.00000.00000.5000
iAMPCN1.00000.50001.00000.75000.66670.57740.8163
EndotoxiniAMP-CA2L0.91670.68750.93750.81250.78570.64550.8125
iAMPCN0.70590.75000.68750.71880.72730.43840.7617
InsecticidalAMAP0.55880.22890.81930.52410.32480.05970.5241
iAMPCN0.85140.75900.86750.81330.80250.63020.8936
ActivityMethodPrecisionSensitivitySpecificityAccuracyF1MCCAUC
AntibacterialAMAP0.57880.87500.36330.61920.69670.27740.6192
AMPDiscover-RF0.61620.88030.45180.66600.72500.36750.6322
AMPDiscover-RNN0.61320.87270.44950.66110.72030.35570.6611
iAMP-CA2L0.49900.68260.31480.49870.5766-0.00280.4987
iAMPCN0.67090.79140.61180.70160.72620.40990.7621
AntifungalAMAP0.53540.82280.28600.55440.64870.12890.5544
AMPDiscover-RF0.53850.78510.32720.55610.63880.12630.5398
AMPDiscover-RNN0.53160.78950.30440.54690.63540.10730.5469
AMPfun0.59010.57460.60090.58770.58220.17550.6256
dbAMP0.55240.80440.34820.57630.65500.17150.6082
iAMP-CA2L0.50000.21400.78600.50000.29980.00000.5000
iAMP-RAAC0.58500.67630.52020.59820.62730.19890.5982
iAMPCN0.73470.53680.80610.67150.62040.35610.7483
AntiviralAMAP0.30420.23360.46560.34960.2643-0.30920.3496
AMPDiscover-RF0.42830.54320.27490.40910.4790-0.18880.4999
AMPDiscover-RNN0.44470.56830.29020.42930.4989-0.14730.4293
AMPfun0.58620.75020.47050.61030.65820.22990.6653
dbAMP0.53920.86180.26350.56270.66330.15640.6006
iAMP-CA2L0.46150.02430.97170.49800.0461-0.01260.4980
iAMP-RAAC0.61560.66530.58450.62490.63950.25060.6249
iAMPCN0.82480.73080.84480.78780.77500.57940.8865
AnticancerAMAP0.39730.41180.37530.39350.4044-0.21300.3935
AMPfun0.44500.41720.47960.44840.4306-0.10340.4444
dbAMP0.48280.63440.32040.47740.5483-0.04760.4759
iAMP-RAAC0.46580.11720.86560.49140.1873-0.02590.4914
iAMPCN0.68300.76670.64410.70540.72240.41390.7698
Anti-Gram positiveAMPfun0.56070.88650.30540.59600.68690.23590.6304
dbAMP0.55130.82650.32720.57680.66140.17740.6107
iAMP-RAAC0.55900.88790.29950.59370.68600.23170.5937
iAMPCN0.63720.79950.54490.67220.70920.35610.7246
Anti-Gram negativeAMPfun0.56830.88680.32620.60650.69270.25720.6390
dbAMP0.56030.85150.33170.59160.67580.21440.6232
iAMP-RAAC0.56350.85820.33540.59680.68030.22710.5968
iAMPCN0.63350.80580.53380.66980.70930.35290.7212
Anti-mammalian cellsAMPfun0.60240.35740.76410.56080.44860.13300.6163
dbAMP0.53740.64860.44160.54510.58780.09230.5585
iAMP-RAAC0.63640.17690.89890.53790.27680.10960.5379
iAMPCN0.67480.79420.61730.70580.72970.41810.7665
Anti-HIVAMAP0.38790.28300.55350.41820.3273-0.16990.4182
iAMP-CA2L0.33330.00630.98740.49690.0123-0.03250.4969
iAMPCN0.84890.74210.86790.80500.79190.61490.8633
Anti-MRSAiAMP-CA2L0.95650.41510.98110.69810.57890.48060.6981
iAMPCN0.86000.81130.86790.83960.83500.68030.8597
AntiparasiticAMAP0.26920.16090.56320.36210.2014-0.30130.3621
AMPDiscover-RF0.50000.72410.27590.50000.59150.00000.6092
AMPDiscover-RNN0.48410.70110.25290.47700.5728-0.05140.4770
AMPfun0.47500.43680.51720.47700.4551-0.04610.4970
iAMP-CA2L0.40000.02300.96550.49430.0435-0.03440.4943
iAMP-RAAC0.55170.18390.85060.51720.27590.04630.5172
iAMPCN0.75340.63220.79310.71260.68750.43090.7861
AntibiofilmAMAP0.59650.45950.68920.57430.51910.15270.5743
iAMP-CA2L0.85710.08110.98650.53380.14810.15920.5338
iAMPCN0.82430.82430.82430.82430.82430.64860.8667
ChemotacticAMAP0.40000.14290.78570.46430.2105-0.09330.4643
iAMP-CA2L0.00000.00001.00000.50000.00000.00000.5000
iAMPCN1.00000.50001.00000.75000.66670.57740.8163
EndotoxiniAMP-CA2L0.91670.68750.93750.81250.78570.64550.8125
iAMPCN0.70590.75000.68750.71880.72730.43840.7617
InsecticidalAMAP0.55880.22890.81930.52410.32480.05970.5241
iAMPCN0.85140.75900.86750.81330.80250.63020.8936
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