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Bioinformatics Advance Access published online on March 12, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn099
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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.

A Nearest Neighbor Approach for Automated Transporter Prediction and Categorization from Protein Sequences

Haiquan Li , Xinbin Dai and Xuechun Zhao *

Bioinformatics Lab, Plant Biology Division, Samuel Roberts Noble Foundation, Inc. 2510 Sam Noble Parkway, Ardmore, Oklahoma, USA 73401

*To whom correspondence should be addressed. Dr. Xuechun Zhao, E-mail: pzhao{at}noble.org, patrickzhao28{at}yahoo.com


  Abstract

Motivation: Membrane transport proteins play a crucial role in the import and export of ions, small molecules, or macromolecules across biological membranes. Currently, there are a limited number of published computational tools which enable the systematic discovery and categorization of transporters prior to costly experimental validation. To approach this problem, we utilized a nearest neighbor method which seamlessly integrates homologous search and topological analysis into a machine learning framework.

Results: Our approach satisfactorily distinguished 484 transporter families in the Transporter Classification Database, a curated and representative database for transporters. A five-fold crossvalidation on the database achieved a positive classification rate of 72.3% on average. Furthermore, this method successfully detected transporters in seven model and four non-model organisms, ranging from archaean to mammalian species. A preliminary literature-based validation has cross-validated 65.8% of our predictions on the eleven organisms, including 55.9% of our predictions overlapping with 83.6% of the predicted transporters in TransportDB.

Availability & Supplementary Information: http://bioinfo.noble.org/manuscript-support/transporter/

Contact: hqli{at}noble.org, xdai{at}noble.org, pzhao{at}noble.org

Associate Editor: Prof. Burkhard Rost

Received on November 21, 2007; revised on March 10, 2008; accepted on March 11, 2008

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