PTM analysis | Proteomics

Tandem mass spectrometry has become a standard tool for identifying post-translational modifications (PTMs) of proteins. Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and…

PTM analysis steps

Bioinformatics tools

Databases

Most recent bioinformatics tools

PRmePRed
Web

PRmePRed Protein aRginine methylation PRediction

Predicts arginine methylation sites in proteins. PRmePRed is a predictor based…

Predicts arginine methylation sites in proteins. PRmePRed is a predictor based on sequence and structure derived features, using support vector machines (SVMs).

UbiSite
Web

UbiSite

Allows users to identify lysine ubiquitylation sites based on…

Allows users to identify lysine ubiquitylation sites based on MDDLogo-identified substrate motifs. UbiSite permits users to submit their protein sequences through a web-based interface. This tool…

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)…

Most popular analytical software and databases

SwissPalm
Dataset

SwissPalm

A comprehensive, manually curated resource to study protein S-palmitoylation.…

A comprehensive, manually curated resource to study protein S-palmitoylation. SwissPalm currently encompasses more than 5000 S-palmitoylated protein hits from seven species, and contains more than…

KinomeXplorer
Desktop

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.

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