Table 4.

Summary of recently deep learning tools associated with PTM sites prediction.

Tool name	PTM type	Species	Core network model	Evaluation strategy	Benchmark dataset size (modification sites)	Web server/ source code	Published year	Reference
MusiteDeep	Multiple	Human	CNN	5-fold CV	997,687	https://www.musite.net	2017/2020	[30]
PROSPECT	Phosphorylation	Escherichia coli	CNN	10-fold CV and independent test	1,664	*prospect.erc.monash.edu/	2020	[56]
DeepKinZero	Phosphorylation	Human	ZSL	holdout	12,901	*https://github.com/Tastanlab/DeepKinZero	2020	[60]
PhosTransfer	Phosphorylation	–	CNN	holdout	43,785	https://github.com/yxu132/PhosTransfer	2020	[61]
GPS-PBS	Phosphorylation	Multiple	seven-layer DNNs	10-fold CV	4,458	–	2020	[62]
DeepPPSite	Phosphorylation	Mammals and Arabidopsis thaliana	LSTM	10-fold CV	41,436	github.com/saeed344/DeepPPSite	2021	[57]
DeepIPs	Phosphorylation	Human	CNN + LSTM	5-fold CV	10.978	https://lin-group.cn/server/DeepIPs https://github.com/linDing-group/DeepIPs	2021	[63]
PhosIDN	Phosphorylation	Human	Multi-layer DNNs	holdout	more than 160,000	https://github.com/ustchangyuanyang/PhosIDN	2021	[64]
EMBER	Phosphorylation	Multiple	CNN + RNN	5-fold CV	8,389	https://github.com/gomezlab/EMBER	2022	[58]
DNNAce	Acetylation	Multiple	DNN	10-fold CV and independent test	96,372	https://github.com/QUSTAIBBDRC/DNNAce/	2020	[78]
Deep-PLA	Acetylation	Human and Nonhuman	DNN	5- and 10-fold CV	1,331	https://deeppla.cancerbio.info	2020	[79]
MDC-Kace	Acetylation	Multiple	MDC	10-fold CV and independent test	11,583	https://github.com/lianglianggg/MDC-Kace	2020	[80]
DeepTL-Ubi	Ubiquitination	Multiple	CNN	holdout	94,518	github.com/USTC-HIlab/DeepTL-Ubi	2020	[106]
Wang et al.’s work	Ubiquitination	Multiple	CNN	10-fold CV	121,742	*https://github.com/wang-hong-fei/DL-plantubsites-prediction	2020	[105]
UbiComb	Ubiquitination	Multiple	LSTM	10-fold CV	121,742	https://nsclbio.jbnu.ac.kr/tools/UbiComb	2021	[107]
SSMFN	Methylation	Human and Mouse	CNN + LSTM	holdout	6,754	*https://github.com/bharuno/SSMFNMethylation-Analysis	2021	[110]
Malebary et al.’s work	Methylation	Human	CNN	10-fold CV and jackknife	2000	https://github.com/s2018 https://doi.org/1080001/WebServer.git	2022	[14]
RecSNO	S-Nitrosylation	–	BiLSTM	5-fold CV	4,762	https://nsclbio.jbnu.ac.kr/tools/RecSNO/.	2021	[111]
MDCAN-Lys	Succinylation	Human	MDCAN	10-fold CV and independent test	77,418	–	2021	[112]
LSTMCNNsucc	Succinylation	Multiple	LSTM + CNN	holdout	18,593	https://8.129.111.5/	2021	[113]
DeepMal	Malonylation	Multiple	CNN + DNN	10-fold CV and independent test	17,288	https://github.com/QUST-AIBBDRC/DeepMal/	2020	[114]
K_net	Malonylation	Human and Mice	CNN	10-fold CV and SEV	85,204	–	2020	[115]
DeepCSO	S-Sulphenylation	Homo sapiens and Arabidopsis thaliana	LSTMWE	10-fold CV	10,354	*https://www.bioinfogo.org/DeepCSO.	2020	[116]
DeepSSPred	S-Sulphenylation	Homo Sapiens	2D-CNN	jackknife	7,756	*https://github.com/zaheerkhancs/DeepSSPred	2021	[117]
pKcr	Crotonylation	Papaya	CNN	10-fold CV and independent test	58,769	*https://www.bioinfogo.org/pkcr.	2020	[119]
Deep-Kcr	Crotonylation	Human	CNN	10-fold CV	19,928	https://lin-group.cn/server/Deep-Kcr	2020	[120]
DeepKcrot	Crotonylation	Multiple	CNNWE	10-fold CV and independent test	10,702/1,265/2,044/5,995	*https://www.bioinfogo.org/deepkcrot.	2021	[121]
nhKcr	Crotonylation	Human	CNNrgb	10-fold CV and independent test	180,312	https://nhKcr.erc.monash.edu/	2021	[118]
DeepKhib	2-Hydroxyisobutyrylation	Multiple	CNNOH	10-fold CV and independent test	18,946/15,444/12,756/19,330/2,098	*https://www.bioinfogo.org/DeepKhib.	2020	[122]
DeepGlut	Glutarylation	Prokaryotes and Eukaryote	CNN	10-fold CV	4,572	*https://github.com/urmisen/DeepGlut.	2020	[123]
NPalmitoylDeep-PseAAC	N-Palmitoylation	Human	DNN	holdout	4,364	https://mega.nz/#F!s9cSiQIa!1jXO0NmgrhxUqOexmYuouA	2021	[124]
DTL-DephosSite	Dephosphorylation	Human	Bi-LSTM	5-fold CV and independent test	4,956	https://github.com/dukkakc/DTLDephos	2021	[127]
PreCar_Deep	Carbonylation	Human and other Mammals	CNN + BiLSTM	10-fold CV and independent test	5,003	https://github.com/QUST-SHULI/PreCar_Deep/	2021	[125]
He et al.'s work	SUMOylation Ubiquitylation	–	CNN + DNN	10-fold CV	280,731	https://github.com/lijingyimm/MultiUbiSUMO	2021	[126]

Note: *, Link is not working at the time of writing. Multiple, more than three species or PTM types. -, data not available.