A method for predicting in vivo kinase-substrate relationships, that augments intrinsic specificities of kinases with cellular context for kinases and phosphoproteins. Based on the latest human phosphoproteome from the Phospho.ELM and PhosphoSite databases, NetworKIN offers insight into phosphorylation-modulated interaction networks. Via the web interface users can query the database of precomputed kinase-substrate relations or obtain predictions on novel phosphoproteins.
Searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains. Scansite is an application to predict short linear sequence motif sites. It uses position-specific scoring matrices (PSSMs) to predict interaction sites that are important in cellular signaling. This application can also be used to show all potential sites in a given protein or all proteins in a database that contains sites for one or more motifs.
A software package for the prediction of in vivo site-specific kinase-substrate relations mainly from the phosphoproteomic data. This work contributes to the understanding of phosphorylation mechanisms at the systemic level, and provides a powerful methodology for the general analysis of in vivo post-translational modifications regulating sub-proteomes.
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 composition of monomer spectrum (CMS) encoding strategy and support vector machines (SVMs).
A strategy based on functional protein microarrays and bioinformatics to experimentally identify substrates for 289 unique kinases, resulting in 3656 high-quality kinase-substrate relationships (KSRs). The value of this data set is demonstrated through the discovery of a new role for PKA downstream of Btk (Bruton's tyrosine kinase) during B-cell receptor signaling.
Predicts the substrate specificity of kinase domains based on the protein sequences. DeepSignal translates a kinase sequence to its binding substrate sequence profile via encoder network and decoder network components. This software exploits information extracted from protein sequence to determine if each residue should be enhanced or silenced. It can also predict the substrate specificity on SH2 domain proteins.
Retrieves kinase-substrate predictions from NetworKIN algorithm and contains various statistical modules for further analysis. PhosphoSiteAnalyzer is a bioinformatical tool for analyzing (quantitative) phosphoproteome datasets. It has a modular design where each module represents a statistical analysis method for extracting various biological features from the phosphoproteomic data set. It also is a computational tool created with the aim of facilitating complex kinase−substrate network analysis in a user-friendly and user-tailored way.