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Phosphorylation site prediction software tools | Post-translational modification analysis

Phosphorylation is a crucial post-translational protein modification mechanism with important regulatory functions in biological systems. It is catalyzed by a group of enzymes called kinases, each of which recognizes certain target sites in its…
KinomeXplorer
Desktop
Web

KinomeXplorer

An integrated framework for modeling kinase-substrate interactions and aid in…

An integrated framework for modeling kinase-substrate interactions and aid in the design of inhibitor-based follow-up perturbation experiments.

PhosPhAt
Web

PhosPhAt

Contains information on Arabidopsis phosphorylation sites which were identified…

Contains information on Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments by different research groups. Specific information about the peptide…

NetPhos
Web

NetPhos

Produces neural network predictions for serine, threonine and tyrosine…

Produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.

Predikin
Web

Predikin

Predicts substrate specificity of protein kinases. Predikin is a web-server…

Predicts substrate specificity of protein kinases. Predikin is a web-server built from three components: (i) a database of protein kinase substrates that links phosphorylation sites with specific…

iPhos-PseEn
Web

iPhos-PseEn

Identifies the phosphorylation sites in proteins. iPhos-PseEn is a predictor…

Identifies the phosphorylation sites in proteins. iPhos-PseEn is a predictor developed by fusing four different pseudo component approaches (amino acids' disorder scores, nearest neighbors,…

Multi-iPPseEvo
Web

Multi-iPPseEvo

Detects the phosphorylation proteins. Multi-iPPseEvo is a predictor that…

Detects the phosphorylation proteins. Multi-iPPseEvo is a predictor that incorporates the protein sequence evolutionary information into the Chou's general pseudo amino acid composition (PseAAC)…

iPhos-PseEvo
Web

iPhos-PseEvo

Identifies human phosphorylated proteins by incorporating evolutionary…

Identifies human phosphorylated proteins by incorporating evolutionary information into general PseAAC via grey system theory. iPhos-PseEvo is an ensemble classifier and a bioinformatics tool aimed…

IKAP
Desktop

IKAP Inference of Kinase Activities from Phosphoproteomics

Estimates the activities of all kinases that are known to phosphorylate at…

Estimates the activities of all kinases that are known to phosphorylate at least one phosphosite in a phosphoproteomics dataset. IKAP takes information from the PhosphoSitePlus (PSP) database as…

NetPhosBac
Web

NetPhosBac

Predicts bacteria-specific protein phosphorylation. NetPhosBac was tested on…

Predicts bacteria-specific protein phosphorylation. NetPhosBac was tested on the predictions of phosphorylation sites in E. coli proteins on protein and site-specific levels. It shows the advantage…

MusiteDeep
Desktop

MusiteDeep

Serves for kinase-specific phosphorylation site prediction. MusiteDeep provides…

Serves for kinase-specific phosphorylation site prediction. MusiteDeep provides a model training that enables advanced users to train other post-translational modification (PTM) prediction models by…

PhosphoPICK-SNP
Web

PhosphoPICK-SNP

Allows researchers to submit protein sequences and amino acid variants in the…

Allows researchers to submit protein sequences and amino acid variants in the protein. PhosphoPICK-SNP is a web application that permits to analyze non-synonymous single nucleotide variants (nsSNVs)…

OccupancyMS
Desktop

OccupancyMS

Calculates the site stoichiometry of a phospho-sites measured under multiple…

Calculates the site stoichiometry of a phospho-sites measured under multiple conditions with quantitative mass spectrometry (MS). OccupancyMS is a MATLAB algorithm that provides confidence intervals.…

PhosPred-RF
Web

PhosPred-RF

Exploits sequential information from multiple perspectives, and yields a set of…

Exploits sequential information from multiple perspectives, and yields a set of discriminative sequential features that are capable to effectively distinguish true phosphorylation sites from…

RLIMS-P
Web

RLIMS-P Rule-based Literature Mining System for protein Phosphorylation

A rule-based information extraction system. RLIMS-P is an online text-mining…

A rule-based information extraction system. RLIMS-P is an online text-mining tool that provides an interface to identify articles relevant to protein phosphorylation, and presents information on…

PhosphoPICK
Web

PhosphoPICK

A method for predicting kinase substrates using cellular context information,…

A method for predicting kinase substrates using cellular context information, and is currently able to make predictions for 59 human kinases. The method is freely available online as a web server.

SubPhos
Web

SubPhos

An account of the emerging field of subcellular phosphoproteomics where a…

An account of the emerging field of subcellular phosphoproteomics where a support vector machine (SVM) approach was combined with a novel algorithm of discrete wavelet transform (DWT) to facilitate…

PhosphOrtholog
Web

PhosphOrtholog

Enables mapping of thousands of novel and known protein phosphorylation sites…

Enables mapping of thousands of novel and known protein phosphorylation sites across species, accessible through an easy-to-use web interface. This is achieved through pairwise sequence alignment of…

MetaPredPS
Web

MetaPredPS

The meta-prediction server makes use of element predictors from the following…

The meta-prediction server makes use of element predictors from the following phosphorylation site predicting programs: GPS, KinasePhos, NetPhosK, PPSP, PredPhospho and Scansite.

DISPHOS
Web

DISPHOS DISorder-enhanced PHOSphorylation predictor

A web-based tool for the prediction of protein phosphorylation sites. It uses…

A web-based tool for the prediction of protein phosphorylation sites. It uses position-specific amino acid frequencies and disorder information to improve the discrimination between phosphorylation…

PhosphoSVM
Web

PhosphoSVM

Employs Support Vector Machine (SVM) to combine protein secondary structure…

Employs Support Vector Machine (SVM) to combine protein secondary structure information and seven other one-dimensional structural properties. PhosphoSVM is a non-kinase specific protein…

KinasePhos
Web

KinasePhos

Predicts phosphorylation sites within given protein sequences. KinasePhos is a…

Predicts phosphorylation sites within given protein sequences. KinasePhos is a web server that allows user to submit their uncharacterized protein sequences and select the kinase-specific models for…

PTMProber
Web

PTMProber

A homology-based pipeline that allows identification of potential modification…

A homology-based pipeline that allows identification of potential modification sites for most of the proteomes lacking post-translational modifications (PTMs) data. PTMProber provides a unique…

DAPPLE
Web

DAPPLE

Predicts phosphorylation sites in an organism of interest. DAPPLE represents an…

Predicts phosphorylation sites in an organism of interest. DAPPLE represents an alternative method to machine-learning approaches and is based on a direct homology-based approach. It employs…

cPhosBac
Web

cPhosBac

Predicts phosphorylation serine/threonine in bacteria proteins. cPhosBac is…

Predicts phosphorylation serine/threonine in bacteria proteins. cPhosBac is developed with CKSAAP algorithm, which was combined with motif length selection to optimize the prediction, which achieves…

NetPhorest
Desktop
Web

NetPhorest

Predicts upstream kinases and downstream phosphobinding domains in…

Predicts upstream kinases and downstream phosphobinding domains in phosphoproteomics data.

jEcho
Desktop

jEcho

A weight vector to represent the variant contributions of the PTM-flanking…

A weight vector to represent the variant contributions of the PTM-flanking positions and use an evolutionary algorithm to optimize the vector. Even a simple nearest neighbor algorithm with the…

phos_pred
Desktop

phos_pred

To enhance phosphorylation site prediction at all hierarchical levels,…

To enhance phosphorylation site prediction at all hierarchical levels, functional information of proteins, including gene ontology (GO) and protein-protein interaction (PPI), is adopted in addition…

AMS
Desktop

AMS AutoMotif Service

Identifies post-translational modification (PTMs) sites in proteins using only…

Identifies post-translational modification (PTMs) sites in proteins using only sequence information. AMS detects over 80 different types of the single amino acid post-translational modifications in…

Phosphohunter
Desktop

Phosphohunter

Provides analysis of phosphopeptide MS/MS spectra. PhosphoHunter is a Perl…

Provides analysis of phosphopeptide MS/MS spectra. PhosphoHunter is a Perl software and provides a full and automated analysis pipeline, starting from dta files (and a FASTA format database) and…

Rice_Phospho
Web

Rice_Phospho

A rice-specific protein phosphorylation site predictor. We have used support…

A rice-specific protein phosphorylation site predictor. We have used support vector machine (SVM) with amino acid occurrence frequency with composition of k-spaced amino acid pairs (AF-CKSAAP) to…

Musite
Desktop

Musite

A Java-based standalone application for predicting both general and…

A Java-based standalone application for predicting both general and kinase-specific protein phosphorylation sites.

MMFPh
Desktop
Web

MMFPh Maximal Motif Finder for Phosphoproteomics datasets

Identifies all significant maximal motifs in a phosphoproteomics dataset, to…

Identifies all significant maximal motifs in a phosphoproteomics dataset, to summarize the data and help identify involved kinases and characterize their specificities. Tests with both synthetic and…

PHOSFER
Web

PHOSFER PHOsphorylation Site FindER

A random forest-based method for applying phosphorylation data from other…

A random forest-based method for applying phosphorylation data from other organisms to enhance the accuracy of predictions in a target organism. It is applied to phosphorylation sites in soybean.

CRPhos
Desktop
Web

CRPhos

An approach to predict phosphorylation sites from the protein sequence. The…

An approach to predict phosphorylation sites from the protein sequence. The method uses a positive dataset to train a conditional random field (CRF) model.

NetPhosYeast
Web

NetPhosYeast

A neural network-based method for the prediction of protein phosphorylation…

A neural network-based method for the prediction of protein phosphorylation sites in yeast--an important model organism for basic research.

PyTMs
Desktop

PyTMs

A plugin implemented with the commonly used visualization software PyMOL. PyTMs…

A plugin implemented with the commonly used visualization software PyMOL. PyTMs enables users to introduce a set of common post-translational modifications (PTMs) into protein/peptide models and can…

PTMPred
Desktop

PTMPred

A computational resource for the identification of post-translational…

A computational resource for the identification of post-translational modification (PTM) sites. It can be used to predict all types of PTM sites if the user provides the training datasets.

PhosphoRice
Desktop

PhosphoRice

A meta-predictor of rice-specific phosphorylation site, was constructed by…

A meta-predictor of rice-specific phosphorylation site, was constructed by integrating the newly phosphorylation sites predictors, NetPhos2.0, NetPhosK, Kinasephos, Scansite, Disphos and Predphosphos…

pkaPS
Web

pkaPS

Prediction of protein kinase A phosphorylation sites using the simplified…

Prediction of protein kinase A phosphorylation sites using the simplified kinase binding model.

PSEA
Web

PSEA Phosphorylation Set Enrichment Analysis

This service can predict the kinase types and kinase-specific phosphorylation…

This service can predict the kinase types and kinase-specific phosphorylation site for a protein by inputting the amino acid sequence in Fasta format. Each query phosphorylation site (S/T/Y) in…

HMMpTM
Web

HMMpTM

A Hidden Markov Model based method, capable of predicting the topology of…

A Hidden Markov Model based method, capable of predicting the topology of transmembrane proteins and the existence of kinase specific phosphorylation and N/O-linked glycosylation sites along the…

PhoScan
Desktop
Web

PhoScan

A prediction system to predict phosphorylation sites in a…

A prediction system to predict phosphorylation sites in a kinase-family-specific way. Common phosphorylation features and kinase-specific features are extracted from substrate sequences of different…

PlantPhos
Web

PlantPhos

A web tool for predicting potential phosphorylation sites in plant proteins.…

A web tool for predicting potential phosphorylation sites in plant proteins. PlantPhos utilizes hidden Markov models (HMM) built from catalytic kinase motifs in plants to predict potential…

PKIS
Web

PKIS

A protein kinase identification web server is presented for the identification…

A protein kinase identification web server is presented for the identification of the protein kinases responsible for experimentally verified P-sites at high specificity, which incorporates the…

ViralPhos
Web

ViralPhos

A computational method which aims to investigate virus substrate site motifs…

A computational method which aims to investigate virus substrate site motifs and identify potential phosphorylation sites on virus proteins. It is freely available to all interested users.

PPRED
Web

PPRED Phosphorylation PREDictor

Provides an efficient way to identify phosphorylation sites in a given protein…

Provides an efficient way to identify phosphorylation sites in a given protein primary sequence that would be a valuable information for the molecular biologists working on protein phosphorylation…

PostMod
Web

PostMod prediction of Post-translational Modification sites

A simple and effective method to recognize phosphorylation sites by combining…

A simple and effective method to recognize phosphorylation sites by combining sequence patterns and evolutionary information and by applying a novel noise-reducing algorithm. PostMod is remarkable in…

Phos3D
Web

Phos3D

A web server for the prediction of phosphorylation sites (P-sites) in proteins.…

A web server for the prediction of phosphorylation sites (P-sites) in proteins. The approach is based on Support Vector Machines trained on sequence profiles enhanced by information from the spatial…

PPSP
Web

PPSP Prediction of PK-specific Phosphorylation site

A versatile and comprehensive program deployed with approach of Bayesian…

A versatile and comprehensive program deployed with approach of Bayesian decision theory (BDT). It could predict the potential phosphorylation sites accurately for approximately 70 PK (Protein…

GPS
Desktop

GPS Group-based Prediction System

A kinase-specific phosphorylation sites predictor with a novel but simple…

A kinase-specific phosphorylation sites predictor with a novel but simple approach of motif length selection (MLS).

MoDL
Desktop

MoDL Motif Description Length

Identifies mixtures of protein phosphorylation motifs. MoDL is based on the…

Identifies mixtures of protein phosphorylation motifs. MoDL is based on the principle of minimum description length (MDL) from information theory. It can create a set of motifs that succinctly…

GPS-Polo
Web
Desktop

GPS-Polo

Predicts Polo-like kinase (Plk) phospho-binding and phosphorylation sites.…

Predicts Polo-like kinase (Plk) phospho-binding and phosphorylation sites. GPS-Polo is an integrated computational platform that provides a method for an easy understanding of Plk-mediated…

PeptideMap
Web

PeptideMap

A tool for finding modifications on polypeptide sequences. The modifications…

A tool for finding modifications on polypeptide sequences. The modifications can be affecting single amino acids (e.g. phosphorylation or oxidation) or cross-linking two amino acids (e.g. disulfide…

NetPhosK
Web

NetPhosK

Produces neural network predictions of kinase specific eukaryotic protein…

Produces neural network predictions of kinase specific eukaryotic protein phosphoylation sites.

PHOXTRACK
Web

PHOXTRACK PHOsphosite-XTRacing Analysis of Causal Kinases

An efficient tool for extracting posttranslational information of comprehensive…

An efficient tool for extracting posttranslational information of comprehensive proteomics datasets to decipher key regulatory proteins and to infer biologically relevant molecular pathways.

PHOSITE
Desktop

PHOSITE

Predicts phosphorylation sites applicable to protein sequences. PHOSITE allows…

Predicts phosphorylation sites applicable to protein sequences. PHOSITE allows the user to tailor the prediction properties. This enables the user to achieve results depending on the favoured…

PredPhospho
Desktop

PredPhospho

Predicts the changes in phosphorylation sites caused by amino acid variations…

Predicts the changes in phosphorylation sites caused by amino acid variations at intra- and interspecies levels. PredPhospho enables users to predict phosphorylation sites in protein sequences using…

CKSAAP_PhSite
Web

CKSAAP_PhSite

A bioinformatics tool was developed that ignored the kinase information and…

A bioinformatics tool was developed that ignored the kinase information and only used the primary sequence information to predict protein phosphorylation sites.

MAP Kinase analyser
Desktop

MAP Kinase analyser Mitogen Activated Protein Kinase

Identifies P-Site, phosphorylation site consensus sequences and domain of the…

Identifies P-Site, phosphorylation site consensus sequences and domain of the Mitogen Activated Protein Kinase (MAPK) in plant genome. MAP Kinase analyser can recognize if the given protein sequence…

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