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PEDS Advance Access published online on February 1, 2009
Protein Engineering Design and Selection, doi:10.1093/protein/gzn084
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

Protein classification combining surface analysis and primary structure

Loris Nanni1,3, Saveria Mazzara2, Linda Pattini2 and Alessandra Lumini1

1DEIS, Università di Bologna, viale risorgimento 2, 40136 Bologna, Italy 2Department of Bioengineering, IIT Unit, Politecnico di Milano, piazza Leonardo da Vinci 32, 20133 Milano, Italy

3 To whom correspondence should be addressed. E-mail: loris.nanni{at}unibo.it

In this work, we propose a method for protein classification that combines the features extracted from both the primary structure and the surface analysis of a given protein. The surface analysis is used to find the amino acids that belong to the surface of the proteins. The most important finding of this work is to show that the features extracted from the amino acids that belong to the surface are useful in the classification process, since their contribution is partially independent from that of the features extracted from the whole primary structure; this property is used to build an ensemble of classifiers. The experimental results demonstrate the effectiveness of the proposed system. The idea is validated using three different data sets and three different feature extraction methods: 2-gram; residue couple; pseudo amino acid composition.

Keywords: fusion of classifiers/protein surface/pseudo amino acid composition

Received June 4, 2008; revised November 14, 2008; accepted December 30, 2008.


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