Table 1
Open in new tab

A comprehensive summary of the reviewed approaches for AMP prediction

TypeToolYearAlgorithmFeature selectionEvaluation strategyWeb server availabilityMax data uploadFile upload availabilityEmail of resultSoftware availability
Machine learning-based methodsAMPer2007HMMsNone10-fold CVNoN.A.N.A.N.A.Yes
 CAMP2010, 2016SVM, RF, ANN, DARFE (RF Gini)10-fold CV, independent testYesN.A.YesNoNo
 Porto et al.2010SVMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 Song et al.2011k-NN, BLASTPmRMR, IFSJack-knife validation, independent testNoN.A.N.A.N.A.No
 Torrent et al.2011ANNNoneIndependent testNoN.A.N.A.N.A.No
 Fernandes et al.2012ANFISANFISIndependent testNoN.A.N.A.N.A.No
 ClassAMP2012RF, SVMRFE (RF Gini)10-fold CV, independent testYesN.A.YesNoNo
 CS-AMPPred2012SVMNone5-fold CV, independent testNoN.A.N.A.N.A.Yes
 C-PAmP2013SVMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 iAMP-2L2013FKNNNoneJack-knife validation, independent testYes500NoNoNo
 Paola et al.2013SVMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 Randou et al.2013LRNoneIndependent testNoN.A.N.A.N.A.No
 dbaasp2014z-ScoreNoneIndependent testNoN.A.N.A.N.A.No
 ADAM2015SVM, profile HMMsNoneN.A.YesN.A.NoNONo
 Camacho et al.2015NB, RF, SVMNone5-fold CV, independent testNoN.A.N.A.N.A.No
 Ng et al.2015SVM, BLASTPNoneJack-knife validation, independent testNoN.A.N.A.N.A.No
 MLAMP2016RFNoneJack-knife validation, independent testYes5YesYesNo
 iAMPpred2017SVMNone10-fold CV, independent testYesN.A.NoNoNo
 AmPEP2018RFNone10-fold CV, independent testYesN.A.YesYesYes
 CLN-MLEM22018MLEM2, IRIMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 MOEA-FW2018RF, k-NN, SVM, ANNNone10-fold CVNoN.A.N.A.N.A.No
 AMAP2019SVM, XGBoost, one-versus-rest classifier fusionNoneLOCO, 5-fold CV, independent testYesN.A.NoNoNo
 MAMPs-Pred2019RF, LC-RF, PS-RFNone10-fold CV, independent testNoN.A.N.A.N.A.No
 dbAMP2019RFNone5-fold CV, independent testNoN.A.N.A.N.A.No
 AMPfun2019DT, RF, SVMFS10-fold CV, independent testYesN.A.NoNoNo
 Ampir2020SVMRFEindependent testNoN.A.N.A.N.A.Yes
 Chung et al.2020RFOneR, FS5-fold CV, independent testNoN.A.N.A.N.A.No
 Fu et al.2020ADANone5-fold CV, independent testNoN.A.N.A.N.A.No
 AmpGram2020RFNone5-fold CV, benchmark testYes50YesNoYes
 IAMPE2020RF, SVM, XGBoost, k-NN, NBNone10-fold CV, independent testYesN.A.YesNoNo
Deep learning-based methodsAMP Scanner V22018LSTMNone10-fold CV, independent testYes50 000YesNoNo
 APIN2019CNNNone10-fold CV, independent testNoN.A.N.A.N.A.Yes
 Deep-AmPEP302020CNNNone10-fold CV, independent testYesN.A.YesYesNo
 AMPlify2020Bi-LSTM, attention mechanismNone5-fold CV, independent testNoN.A.N.A.N.A.Yes
TypeToolYearAlgorithmFeature selectionEvaluation strategyWeb server availabilityMax data uploadFile upload availabilityEmail of resultSoftware availability
Machine learning-based methodsAMPer2007HMMsNone10-fold CVNoN.A.N.A.N.A.Yes
 CAMP2010, 2016SVM, RF, ANN, DARFE (RF Gini)10-fold CV, independent testYesN.A.YesNoNo
 Porto et al.2010SVMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 Song et al.2011k-NN, BLASTPmRMR, IFSJack-knife validation, independent testNoN.A.N.A.N.A.No
 Torrent et al.2011ANNNoneIndependent testNoN.A.N.A.N.A.No
 Fernandes et al.2012ANFISANFISIndependent testNoN.A.N.A.N.A.No
 ClassAMP2012RF, SVMRFE (RF Gini)10-fold CV, independent testYesN.A.YesNoNo
 CS-AMPPred2012SVMNone5-fold CV, independent testNoN.A.N.A.N.A.Yes
 C-PAmP2013SVMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 iAMP-2L2013FKNNNoneJack-knife validation, independent testYes500NoNoNo
 Paola et al.2013SVMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 Randou et al.2013LRNoneIndependent testNoN.A.N.A.N.A.No
 dbaasp2014z-ScoreNoneIndependent testNoN.A.N.A.N.A.No
 ADAM2015SVM, profile HMMsNoneN.A.YesN.A.NoNONo
 Camacho et al.2015NB, RF, SVMNone5-fold CV, independent testNoN.A.N.A.N.A.No
 Ng et al.2015SVM, BLASTPNoneJack-knife validation, independent testNoN.A.N.A.N.A.No
 MLAMP2016RFNoneJack-knife validation, independent testYes5YesYesNo
 iAMPpred2017SVMNone10-fold CV, independent testYesN.A.NoNoNo
 AmPEP2018RFNone10-fold CV, independent testYesN.A.YesYesYes
 CLN-MLEM22018MLEM2, IRIMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 MOEA-FW2018RF, k-NN, SVM, ANNNone10-fold CVNoN.A.N.A.N.A.No
 AMAP2019SVM, XGBoost, one-versus-rest classifier fusionNoneLOCO, 5-fold CV, independent testYesN.A.NoNoNo
 MAMPs-Pred2019RF, LC-RF, PS-RFNone10-fold CV, independent testNoN.A.N.A.N.A.No
 dbAMP2019RFNone5-fold CV, independent testNoN.A.N.A.N.A.No
 AMPfun2019DT, RF, SVMFS10-fold CV, independent testYesN.A.NoNoNo
 Ampir2020SVMRFEindependent testNoN.A.N.A.N.A.Yes
 Chung et al.2020RFOneR, FS5-fold CV, independent testNoN.A.N.A.N.A.No
 Fu et al.2020ADANone5-fold CV, independent testNoN.A.N.A.N.A.No
 AmpGram2020RFNone5-fold CV, benchmark testYes50YesNoYes
 IAMPE2020RF, SVM, XGBoost, k-NN, NBNone10-fold CV, independent testYesN.A.YesNoNo
Deep learning-based methodsAMP Scanner V22018LSTMNone10-fold CV, independent testYes50 000YesNoNo
 APIN2019CNNNone10-fold CV, independent testNoN.A.N.A.N.A.Yes
 Deep-AmPEP302020CNNNone10-fold CV, independent testYesN.A.YesYesNo
 AMPlify2020Bi-LSTM, attention mechanismNone5-fold CV, independent testNoN.A.N.A.N.A.Yes

Full names of the algorithms: N.A., not available; HMMs, hidden Markov models; SVM, support vector machine; RF, random forest; ANN, artificial neural networks; DA, discriminant analysis; DT, decision tree; LR, logistic regression; k-NN, k-nearest neighbor; BLASTP, basic local alignment search tool (protein); ANFIS, adaptive neuro-fuzzy inference system; NB, naive Bayes; FKNN, fuzzy k-nearest neighbor; profile HMMs, profile hidden Markov models; MLEM2, modified learning from examples module; IRIM, interesting rule induction module; XGBoost, extreme gradient boosting; PS-RF, pruned sets-random forests; LC-RF, label combination-random forests; ADA, adaboost; LSTM, long short-term memory; CNN, convolutional neural networks; Bi-LSTM, bidirectional LSTM.

Table 1
Open in new tab

A comprehensive summary of the reviewed approaches for AMP prediction

TypeToolYearAlgorithmFeature selectionEvaluation strategyWeb server availabilityMax data uploadFile upload availabilityEmail of resultSoftware availability
Machine learning-based methodsAMPer2007HMMsNone10-fold CVNoN.A.N.A.N.A.Yes
 CAMP2010, 2016SVM, RF, ANN, DARFE (RF Gini)10-fold CV, independent testYesN.A.YesNoNo
 Porto et al.2010SVMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 Song et al.2011k-NN, BLASTPmRMR, IFSJack-knife validation, independent testNoN.A.N.A.N.A.No
 Torrent et al.2011ANNNoneIndependent testNoN.A.N.A.N.A.No
 Fernandes et al.2012ANFISANFISIndependent testNoN.A.N.A.N.A.No
 ClassAMP2012RF, SVMRFE (RF Gini)10-fold CV, independent testYesN.A.YesNoNo
 CS-AMPPred2012SVMNone5-fold CV, independent testNoN.A.N.A.N.A.Yes
 C-PAmP2013SVMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 iAMP-2L2013FKNNNoneJack-knife validation, independent testYes500NoNoNo
 Paola et al.2013SVMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 Randou et al.2013LRNoneIndependent testNoN.A.N.A.N.A.No
 dbaasp2014z-ScoreNoneIndependent testNoN.A.N.A.N.A.No
 ADAM2015SVM, profile HMMsNoneN.A.YesN.A.NoNONo
 Camacho et al.2015NB, RF, SVMNone5-fold CV, independent testNoN.A.N.A.N.A.No
 Ng et al.2015SVM, BLASTPNoneJack-knife validation, independent testNoN.A.N.A.N.A.No
 MLAMP2016RFNoneJack-knife validation, independent testYes5YesYesNo
 iAMPpred2017SVMNone10-fold CV, independent testYesN.A.NoNoNo
 AmPEP2018RFNone10-fold CV, independent testYesN.A.YesYesYes
 CLN-MLEM22018MLEM2, IRIMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 MOEA-FW2018RF, k-NN, SVM, ANNNone10-fold CVNoN.A.N.A.N.A.No
 AMAP2019SVM, XGBoost, one-versus-rest classifier fusionNoneLOCO, 5-fold CV, independent testYesN.A.NoNoNo
 MAMPs-Pred2019RF, LC-RF, PS-RFNone10-fold CV, independent testNoN.A.N.A.N.A.No
 dbAMP2019RFNone5-fold CV, independent testNoN.A.N.A.N.A.No
 AMPfun2019DT, RF, SVMFS10-fold CV, independent testYesN.A.NoNoNo
 Ampir2020SVMRFEindependent testNoN.A.N.A.N.A.Yes
 Chung et al.2020RFOneR, FS5-fold CV, independent testNoN.A.N.A.N.A.No
 Fu et al.2020ADANone5-fold CV, independent testNoN.A.N.A.N.A.No
 AmpGram2020RFNone5-fold CV, benchmark testYes50YesNoYes
 IAMPE2020RF, SVM, XGBoost, k-NN, NBNone10-fold CV, independent testYesN.A.YesNoNo
Deep learning-based methodsAMP Scanner V22018LSTMNone10-fold CV, independent testYes50 000YesNoNo
 APIN2019CNNNone10-fold CV, independent testNoN.A.N.A.N.A.Yes
 Deep-AmPEP302020CNNNone10-fold CV, independent testYesN.A.YesYesNo
 AMPlify2020Bi-LSTM, attention mechanismNone5-fold CV, independent testNoN.A.N.A.N.A.Yes
TypeToolYearAlgorithmFeature selectionEvaluation strategyWeb server availabilityMax data uploadFile upload availabilityEmail of resultSoftware availability
Machine learning-based methodsAMPer2007HMMsNone10-fold CVNoN.A.N.A.N.A.Yes
 CAMP2010, 2016SVM, RF, ANN, DARFE (RF Gini)10-fold CV, independent testYesN.A.YesNoNo
 Porto et al.2010SVMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 Song et al.2011k-NN, BLASTPmRMR, IFSJack-knife validation, independent testNoN.A.N.A.N.A.No
 Torrent et al.2011ANNNoneIndependent testNoN.A.N.A.N.A.No
 Fernandes et al.2012ANFISANFISIndependent testNoN.A.N.A.N.A.No
 ClassAMP2012RF, SVMRFE (RF Gini)10-fold CV, independent testYesN.A.YesNoNo
 CS-AMPPred2012SVMNone5-fold CV, independent testNoN.A.N.A.N.A.Yes
 C-PAmP2013SVMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 iAMP-2L2013FKNNNoneJack-knife validation, independent testYes500NoNoNo
 Paola et al.2013SVMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 Randou et al.2013LRNoneIndependent testNoN.A.N.A.N.A.No
 dbaasp2014z-ScoreNoneIndependent testNoN.A.N.A.N.A.No
 ADAM2015SVM, profile HMMsNoneN.A.YesN.A.NoNONo
 Camacho et al.2015NB, RF, SVMNone5-fold CV, independent testNoN.A.N.A.N.A.No
 Ng et al.2015SVM, BLASTPNoneJack-knife validation, independent testNoN.A.N.A.N.A.No
 MLAMP2016RFNoneJack-knife validation, independent testYes5YesYesNo
 iAMPpred2017SVMNone10-fold CV, independent testYesN.A.NoNoNo
 AmPEP2018RFNone10-fold CV, independent testYesN.A.YesYesYes
 CLN-MLEM22018MLEM2, IRIMNone10-fold CV, independent testNoN.A.N.A.N.A.No
 MOEA-FW2018RF, k-NN, SVM, ANNNone10-fold CVNoN.A.N.A.N.A.No
 AMAP2019SVM, XGBoost, one-versus-rest classifier fusionNoneLOCO, 5-fold CV, independent testYesN.A.NoNoNo
 MAMPs-Pred2019RF, LC-RF, PS-RFNone10-fold CV, independent testNoN.A.N.A.N.A.No
 dbAMP2019RFNone5-fold CV, independent testNoN.A.N.A.N.A.No
 AMPfun2019DT, RF, SVMFS10-fold CV, independent testYesN.A.NoNoNo
 Ampir2020SVMRFEindependent testNoN.A.N.A.N.A.Yes
 Chung et al.2020RFOneR, FS5-fold CV, independent testNoN.A.N.A.N.A.No
 Fu et al.2020ADANone5-fold CV, independent testNoN.A.N.A.N.A.No
 AmpGram2020RFNone5-fold CV, benchmark testYes50YesNoYes
 IAMPE2020RF, SVM, XGBoost, k-NN, NBNone10-fold CV, independent testYesN.A.YesNoNo
Deep learning-based methodsAMP Scanner V22018LSTMNone10-fold CV, independent testYes50 000YesNoNo
 APIN2019CNNNone10-fold CV, independent testNoN.A.N.A.N.A.Yes
 Deep-AmPEP302020CNNNone10-fold CV, independent testYesN.A.YesYesNo
 AMPlify2020Bi-LSTM, attention mechanismNone5-fold CV, independent testNoN.A.N.A.N.A.Yes

Full names of the algorithms: N.A., not available; HMMs, hidden Markov models; SVM, support vector machine; RF, random forest; ANN, artificial neural networks; DA, discriminant analysis; DT, decision tree; LR, logistic regression; k-NN, k-nearest neighbor; BLASTP, basic local alignment search tool (protein); ANFIS, adaptive neuro-fuzzy inference system; NB, naive Bayes; FKNN, fuzzy k-nearest neighbor; profile HMMs, profile hidden Markov models; MLEM2, modified learning from examples module; IRIM, interesting rule induction module; XGBoost, extreme gradient boosting; PS-RF, pruned sets-random forests; LC-RF, label combination-random forests; ADA, adaboost; LSTM, long short-term memory; CNN, convolutional neural networks; Bi-LSTM, bidirectional LSTM.

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