Abstract
BackgroundWe have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. The method, named Predikin, identifies key conserved substrate-determining residues in the kinase catalytic domain that contact the substrate in the region of the phosphorylation site and so determine the sequence surrounding the phosphorylation site. Predikin was implemented originally as a web application written in Javascript.ResultsHere, we describe a new version of Predikin, completely revised and rewritten as a modular framework that provides multiple enhancements compared with the original. Predikin now consists of two components: (i) PredikinDB, a database of phosphorylation sites that links substrates to kinase sequences and (ii) a Perl module, which provides methods to classify protein kinases, reliably identify substrate-determining residues, generate scoring matrices and score putative phosphorylation sites in query sequences. The performance of Predikin as measured using receiver operator characteristic (ROC) graph analysis equals or surpasses that of existing comparable methods. The Predikin website has been redesigned to incorporate the new features.ConclusionNew features in Predikin include the use of SQL queries to PredikinDB to generate predictions, scoring of predictions, more reliable identification of substrate-determining residues and putative phosphorylation sites, extended options to handle protein kinase and substrate data and an improved web interface. The new features significantly enhance the ability of Predikin to analyse protein kinases and their substrates. Predikin is available at .
Highlights
We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases
For each kinase-substrate pair in the test set, Predikin substrate-determining residue (SDR), Kinase Sequence Database (KSD) and Protein Analysis Through Evolutionary Relationships (PANTHER) scores were calculated for all X3 [STY]X3 sites in the substrate, using homology reduction when building the scoring matrices
The procedure generated a set of ten files, containing scored and labelled sites for each of the three scoring methods (SDR, KSD or PANTHER) and for each kinase type
Summary
We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. The method, named Predikin, identifies key conserved substratedetermining residues in the kinase catalytic domain that contact the substrate in the region of the phosphorylation site and so determine the sequence surrounding the phosphorylation site. BMC Bioinformatics 2008, 9:245 http://www.biomedcentral.com/1471-2105/9/245 substrates regulate essentially all cellular processes through complex regulatory networks, in which phosphorylated proteins act as switches that tune the response of the cell to environmental stimuli. Defects in these networks result in a variety of disease states making protein kinases important targets for drug design [3]. The heptapeptide sequence from -3 to +3 that best binds to the pocket is determined by the physicochemical nature of the residues in the catalytic domain that line the pocket and contact the substrate
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