Table 3.

Available phosphorylation site and kinase-substrate prediction tools

Tool	Last update	Version	Prediction type	Method	Kinases/phosphatases	Type	References
DISPHOS	2004	1.3	Phosphorylation sites	Bagged logistic regression	0	Web	[54]
PPSP	2006	1.06	Phosphorylation sites of kinases	Bayesian decision theory	68	Web	[52]
KinasePhos2.0	2007	2.0	Phosphorylation sites of kinases	SVM	58	Web	[51]
pkaPS	2007		Phosphorylation sites of PKA	Scoring function	1	Web|DL	[72]
PhoScan	2008		Phosphorylation sites of kinases	Scoring function	48	Web|Tool	[60]
Phos3D	2009		Phosphorylation sites and some kinase specificity	SVM	5	Web	[55]
Musite	2010	1	Phosphorylation sites and some kinase specificity	SVM	13	Web|DL	[62]
PHOSIDA Predictor	2011	3.24	Phosphorylation S and T sites	SVM	0	Web	[26]
Predikin	2011		Phosphorylation sites of kinases	PSSM	any	Web|DL	[53]
GPS-Polo	2012	1.0	Phosphorylation sites of Plk	Group-based scoring function PSSM	1	Web|Tool	[120]
iGPS	2012	1.0.1	Phosphorylation sites of kinases in vivo	GPS with PPI	407	Tool	[57]
CEASAR	2013		Kinases for known phosphorylation sites	Naïve Bayes	289	DL	[56]
HMMpTM	2013		Phosphorylation sites of kinases and topology	HMM	9	Web|DL	[121]
PKIS	2013		Phosphorylation sites of kinases	SVM	56	Web	[122]
GPS	2014	5.0	Phosphorylation sites of kinases	Group-based scoring function PSSM	464	Web|DL|Tool	[61]
NetPhorest	2014	2.1	Phosphorylation sites of kinases	ANN and PSSM	244	Web|DL|Tool	[58, 65]
NetworKIN	2014	3.0	Phosphorylation sites of kinases in vivo	Naïve Bayes with PPI	123	Web|DL|Tool	[58, 66]
phos_pred	2014		Predicts phosphorylation sites for kinases	Random forest	54	Toola	[49]
PhosphoSVM	2014		Phosphorylation sites	SVM	0	Web	[123]
Ptpset	2014		Dephosphorylation sites of phosphatases	KNN	3	Web	[124]
jEcho	2015	1.0	Phosphorylation sites of kinases	Weight vector	12	Tool	[68]
KSP-PUEL	2015		Phosphorylation sites of kinases	SVM ensemble	2a	Tool	[63]
Scansite	2015	4	Kinase motifs in proteins	PSSM	70	Web|DL	[125]
DAPPLE	2016	2	Phosphorylation sites	BLAST	0	Web|DL	[126]
iPhos-PseEn	2016		Phosphorylation sites	Random forest ensemble	0	Web	[127]
PhosphoPICK	2016		Phosphorylation sites of kinases	Bayesian network	107	Web|DL	[70]
PhosD	2016		Kinase-substrate relationships	Probabilistic model	399	DL	[128]
MusiteDeep	2017		Phosphorylation sites and some kinase specificity	DNN	5	Toola	[50]
NetPhos	2017	3.1	Phosphorylation sites and some kinase specificity	ANN	17	Web|Toola	[59, 71]
PhosphoNET	2017		Phosphorylation sites of kinases	PSSM	488	Web	[43]
PhosPred-RF	2017		Phosphorylation sites	Random forest	0	Web	[129]
AKID	2018		Phosphorylation sites of kinases	DNN	496	Web|DL|Toola	[69]
CapsNet_PTM	2018		Phosphorylation sites and some kinase specificity	DNN	any	Tool	[130]
PTM-ssMP	2018		Phosphorylation sites and some kinase specificity	SVM	9	Web|DL	[131]
Quokka	2018		Phosphorylation sites of kinase families	Logistic regression	65	Web|DL	[132]
TyrPred	2018		Phosphorylation sites of Tyr kinases	Elastic net	15	Web	[133]
CoPhosK	2019		Kinases of phosphorylation sites	Naïve Bayes	101	Web|Tool	[134]
DeepPhos	2019		Phosphorylation sites and some kinase specificity	DNN	20	Tool	[67]

^aIndicates number of trained kinases, but tool can be trained with others

SVM support vector machine, PSSM position specific scoring matrix, GSEA gene set enrichment analysis, ANN artificial neural network, DNN deep neural network, HMM hidden Markov model, PPI protein–protein interaction, KNN K-nearest neighbor

^aIndicates tool is not available for all three main operating systems (Linux, Mac, Windows)