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Nucleic Acids Research Advance Access published online on May 13, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn279
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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The Predikin webserver: improved prediction of protein kinase peptide specificity using structural information

Neil F. W. Saunders1,* and Bostjan Kobe2

1School of Molecular and Microbial Sciences and 2Institute for Molecular Bioscience and Special Research Centre for Functional and Applied Genomics, University of Queensland, Brisbane 4072, Australia

*To whom correspondence should be addressed. Tel: +61 7 3365 4866; Fax: +61 7 3365 4699; Email: n.saunders{at}uq.edu.au Correspondence may also be addressed to Bostjan Kobe. Tel: +61 7 3365 2132; Fax: +61 7 3365 4699; Email: b.kobe{at}uq.edu.au

Received January 31, 2008. Revised April 24, 2008. Accepted April 26, 2008.

The Predikin webserver allows users to predict substrates of protein kinases. The Predikin system is built from three components: a database of protein kinase substrates that links phosphorylation sites with specific protein kinase sequences; a perl module to analyse query protein kinases and a web interface through which users can submit protein kinases for analysis. The Predikin perl module provides methods to (i) locate protein kinase catalytic domains in a sequence, (ii) classify them by type or family, (iii) identify substrate-determining residues, (iv) generate weighted scoring matrices using three different methods, (v) extract putative phosphorylation sites in query substrate sequences and (vi) score phosphorylation sites for a given kinase, using optional filters. The web interface provides user-friendly access to each of these functions and allows users to obtain rapidly a set of predictions that they can export for further analysis. The server is available at http://predikin.biosci.uq.edu.au.


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