Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated da

Background: 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. Predikin was implemented originally as a web application written in Javascript. Results: Here, 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 ...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Neil F. W. Saunders, Ross I. Brinkworth, Thomas Huber, Bruce E. Kemp, Bostjan Kobe
• Keywords: BMCBI 2008, Phosphorylation Sites, Protein Kinases, Putative Phosphorylation Sites