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 | Â | Phosphorylation sites of PKA | Scoring function | 1 | Web|DL | [72] |
PhoScan | 2008 | Â | Phosphorylation sites of kinases | Scoring function | 48 | Web|Tool | [60] |
Phos3D | 2009 | Â | 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 | Â | 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 | Â | Phosphorylation sites of kinases and topology | HMM | 9 | Web|DL | [121] |
PKIS | 2013 | Â | 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 | |
NetworKIN | 2014 | 3.0 | Phosphorylation sites of kinases in vivo | Naïve Bayes with PPI | 123 | Web|DL|Tool | |
phos_pred | 2014 | Â | Predicts phosphorylation sites for kinases | Random forest | 54 | Toola | [49] |
PhosphoSVM | 2014 | Â | Phosphorylation sites | SVM | 0 | Web | [123] |
Ptpset | 2014 | Â | Dephosphorylation sites of phosphatases | KNN | 3 | Web | [124] |
jEcho | 2015 | 1.0 | Phosphorylation sites of kinases | Weight vector | 12 | Tool | [68] |
KSP-PUEL | 2015 | Â | 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 | Â | Phosphorylation sites | Random forest ensemble | 0 | Web | [127] |
PhosphoPICK | 2016 | Â | Phosphorylation sites of kinases | Bayesian network | 107 | Web|DL | [70] |
PhosD | 2016 | Â | Kinase-substrate relationships | Probabilistic model | 399 | DL | [128] |
MusiteDeep | 2017 | Â | Phosphorylation sites and some kinase specificity | DNN | 5 | Toola | [50] |
NetPhos | 2017 | 3.1 | Phosphorylation sites and some kinase specificity | ANN | 17 | Web|Toola | |
PhosphoNET | 2017 | Â | Phosphorylation sites of kinases | PSSM | 488 | Web | [43] |
PhosPred-RF | 2017 | Â | Phosphorylation sites | Random forest | 0 | Web | [129] |
AKID | 2018 | Â | Phosphorylation sites of kinases | DNN | 496 | Web|DL|Toola | [69] |
CapsNet_PTM | 2018 | Â | Phosphorylation sites and some kinase specificity | DNN | any | Tool | [130] |
PTM-ssMP | 2018 | Â | Phosphorylation sites and some kinase specificity | SVM | 9 | Web|DL | [131] |
Quokka | 2018 | Â | Phosphorylation sites of kinase families | Logistic regression | 65 | Web|DL | [132] |
TyrPred | 2018 | Â | Phosphorylation sites of Tyr kinases | Elastic net | 15 | Web | [133] |
CoPhosK | 2019 |  | Kinases of phosphorylation sites | Naïve Bayes | 101 | Web|Tool | [134] |
DeepPhos | 2019 | Â | Phosphorylation sites and some kinase specificity | DNN | 20 | Tool | [67] |