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Bioinformatics Advance Access published online on April 4, 2006
Bioinformatics, 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
Received July 11, 2005
Revised March 30, 2006
Accepted March 31, 2006

Article

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.
Burkhard Heil, E-mail: Burkhard.Heil{at}gmail.com


  Abstract

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 of 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 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.

Associate Editor: Alfonso Valencia
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