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Table 3 Available phosphorylation site and kinase-substrate prediction tools

From: Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources

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]

  1. aIndicates number of trained kinases, but tool can be trained with others
  2. 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
  3. aIndicates tool is not available for all three main operating systems (Linux, Mac, Windows)