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Bioinformatics Advance Access originally published online on April 4, 2006
Bioinformatics 2006 22(13):1562-1568; doi:10.1093/bioinformatics/btl132
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Computational recognition of potassium channel sequences

Burkhard Heil 1,*, Jost Ludwig 1, Hella Lichtenberg-Fraté 1 and Thomas Lengauer 2

1 Universität Bonn, IZMB Kirschallee 1, 53115 Bonn, Germany
2 Max Planck Institut für Informatik, Stuhlsatzenhausweg 85 66123 Saarbrücken, Germany

*To whom correspondence should be addressed.

Motivation: Potassium channels are mainly known for their role in regulating and maintaining the membrane potential. Since this is one of the key mechanisms of signal transduction, malfunction of these potassium channels leads to a wide variety of severe diseases. Thus potassium channels are priority targets of research for new drugs, despite the fact that this protein family is highly variable and closely related to other channels, which makes it very difficult to identify new types of potassium channel sequences.

Results: Here we present a new method for identifying potassium channel sequences (PSM, Property Signature Method), which—in contrast to the known methods for protein classification—is directly based on physicochemical properties of amino acids rather than on the amino acids themselves. A signature for the pore region including the selectivity filter has been created, representing the most common physicochemical properties of known potassium channels. This string enables genome-wide screening for sequences with similar features despite a very low degree of amino acid similarity within a protein family.

Availability: The PSM software will be made available on request from the corresponding author.

Contact: Burkhard.Heil{at}gmail.com

Supplementary information: Supplementary data are available at Bioinformatics online.

Received on July 11, 2005; revised on March 30, 2006; accepted on March 31, 2006

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