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BMCBI
2008

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

9 years 3 months ago
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 ...
Neil F. W. Saunders, Ross I. Brinkworth, Thomas Hu
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2008
Where BMCBI
Authors Neil F. W. Saunders, Ross I. Brinkworth, Thomas Huber, Bruce E. Kemp, Bostjan Kobe
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