Phosphorylation site detection software tools | Post-translational modification data 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 substrate proteins.
Produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins. NetPhos is a web application based on determination of the activity of protein kinases using in vitro assays with either naturally occurring peptides or synthetic peptides. This server can assist the experimentalist who wants to design a mutagenesis experiment on a newly found protein of possibly unknown function.
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 sites and for bioinformaticians developing generalized prediction systems for the post translational modifications like phosphorylation or glycosylation. PPRED ignores the kinase information and only uses the evolutionary information of proteins for classifying phosphorylation sites.
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 predicting phosphorylated serine, threonine, tyrosine or histidine. The software incorporates support vector machines (SVM) with two features, i.e. protein sequence profiles surrounding the modified sites and coupling patterns surrounding the modified sites.
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 and non-phosphorylation sites.
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 protein kinase sequences, (ii) a module to analyze query protein kinases, and (iii) a web interface through which users can submit protein kinases for analysis. Users obtain a set of predictions that can be exported for further analysis.
Determines kinase family-specific phosphorylation sites in the human proteome. Quokka employs various sequence-scoring functions and a logistic regression optimization algorithm. It includes the outcomes of sequence scoring functions for each kinase family to construct a logistic regression (LR) model. This tool can be applied for phosphorylation site identification and phosphoproteomic data analysis.