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Bioinformatics Advance Access originally published online on August 5, 2004
Bioinformatics 2004 20(18):3620-3627; doi:10.1093/bioinformatics/bth455
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.

Highly specific prediction of phosphorylation sites in proteins

Matthias Koenig 1,* and Niels Grabe 2

1 CeVis, University of Bremen, Universitaetsallee 29, 28359 Bremen, Germany and 2 AgeLab Pharma GmbH, Grandweg 64, 22529 Hamburg, Germany

Received on May 8, 2003; accepted on July 27, 2004
Advance Access Publication August 5, 2004

Summary: The prediction of significant short functional protein sequences has inherent problems. In predicting phosphorylation sites, problems came from the shortness of phosphorylation sites, the difficulties in maintaining many different predefined models of binding sites, and the difficulties of obtaining highly sensitive predictions and of obtaining predictions with a constant sensitivity and specificity. The algorithm presented in this paper overcomes these problems.

The proposed algorithm PHOSITE is based on the case-based sequence analysis. This enables the prediction of phosphorylation sites with constant specificity and sensitivity. Furthermore, this method leads not only to the prediction of phosphorylation sites in general but also predicts the most probable type of kinase involved.

Availability: The tool PHOSITE implementing the presented method can be evaluated under the website http://www.phosite.com

Contact: koenig{at}cevis.uni-bremen.de

* To whom correspondence should be addressed.


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