Table 1.

A comprehensive summary of the reviewed approaches for AMP prediction

Category	Tool	Year	Prediction of functional activities	Positive data source	CD-HIT cut-off	Algorithm	Sampling strategy	Feature selection	Evaluation strategy	Evaluation metrics	Webserver/software availability
Machine learning based	iAMP-2L	2013	Antibacterial, anticancer, antiviral, antifungal, anti-HIV	APD2	1st: 40%; 2nd: 40%	FKNN	N.A.	N.A.	Jack-knife validation test, independent test	Acc, Sp, Sn, MCC, macro Pr, macro Sn, macro Acc, SA, HL	Yes
	MLAMP	2016	Antibacterial, anticancer, antifungal, anti-HIV, antiviral	APD2	1st: 40%; 2nd: 40%	RF, ECC	SMOTE	N.A.	Jack-knife validation test, independent test	Acc, Sp, Sn, MCC, macro Pr, macro Sn, macro Acc, SA, HL	Yes
	AMAP	2019	Antibacterial, anticancer, antifungal, anti-HIV, antiviral, antibiofilm, antiparasitic, chemotactic, insecticidal, antimalarial, antioxidant, spermicidal, anti-protist	APD3	1st: N.A.; 2nd: N.A.	SVM, XGB, one-vs-rest classifier fusion	N.A.	N.A.	LOCO, 5-fold CV, independent test	AUC, AUPR, MCC	Yes
	AMPfun	2019	Antiparasitic, anticancer, antifungal, antiviral, targeting mammals, targeting Gram-positive bacteria, targeting Gram-positive bacteria	APD3, ADAM, ParaPep, AVPdb, CancerPPD, MLACP, AntiCP, AntiFP, DRAMP	1st: 50%; 2nd: N.A.	DT, RF, SVM	N.A.	SFS	10-fold CV, independent test	Acc, Sp, Sn, MCC, AUC	Yes
	Zhang et al.’ s work	2020	Anti-MRSA, antibacterial, antiviral, antifungal, anticancer, anti-HIV, antiparasitic	APD3, APD2	1st: 40%; 2nd: 40%	GBDT, ET, ECC	ADASYN	Lasso	10-fold CV, independent test	Acc, Sp, Sn, MCC, macro Pr, macro Sn, macro Acc, HL, AP	No
	iAMP-RAAC	2021	Antiparasitic, anticancer, antifungal, antiviral, targeting mammals, targeting Gram-positive bacteria, targeting Gram-positive bacteria	APD3, ADAM, ParaPep, AVPdb, CancerPPD, MLACP, AntiCP, AntiFP, DRAMP	1st: 50%; 2nd: N.A.	SVM	N.A.	ANOVA, IFS	10-fold CV，independent test	Acc, Sp, Sn, MCC	Yes
	dbAMP 2.0	2021	Anticancer, antifungal, antiviral, targeting mammals, targeting Gram-positive bacteria, targeting Gram-positive bacteria	dbAMP 2.0, APD2, CAMP	1st: 50%; 2nd: N.A.	GBDT	N.A.	N.A.	5-fold CV	Sn, Sp, balanced Acc	Yes
Deep learning based	iAMP-CA2L	2021	Antibacterial, anticancer, antifungal, anti-HIV, antiviral, antibiofilm, antiparasitic, chemotactic, anti-MRSA, antiendotoxin	APD3, AMPer, ADAM	1st: 90%; 2nd: 90%	DL	N.A.	N.A.	Jack-knife validation, independent test	Acc, Pr, Sp, Sn, MCC, F1, SA, AP, coverage, HL, RL, OE, macro Pr, macro Sn, macro F1, micro Pr, micro Sn, micro F1	Yes
	Multi-AMP	2021	Anti-MRSA, antibacterial, antiviral, antifungal, anticancer, anti-HIV, antiparasitic	APD3, APD2	1st: 40%; 2nd: 40%	DL	N.A.	N.A.	5-fold CV, independent test	Acc, Sp, Sn, MCC, F1, macro Sp, macro Sn, macro Acc, HL, macro MCC, macro F1	No
	AMPDiscover	2021	Antibacterial, antifungal, antiviral, antiparasitic	starPepDB	1st: 50%; 2nd: N.A.	RF, DL	N.A.	Correlation subset, SE, Relif-F, IG, gain ratio, symmetrical uncertainty	5-fold CV, 10-fold CV, 15-fold CV, 20-fold CV, 25-fold CV, independent test	Acc, Sp, Sn, MCC, AUC	Yes