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Bioinformatics Advance Access originally published online on May 12, 2008
Bioinformatics 2008 24(15):1662-1668; doi:10.1093/bioinformatics/btn221
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

OCTOPUS: improving topology prediction by two-track ANN-based preference scores and an extended topological grammar

Håkan Viklund * and Arne Elofsson

Department of Biochemistry and Biophysics/Center for Biomembrane Research/Stockholm Bioinformatics Center, The Arrhenius Laboratories for Natural Sciences, Stockholm University SE-10691 Stockholm, Sweden

*To whom correspondence should be addressed.


  Abstract

Motivation: As {alpha}-helical transmembrane proteins constitute roughly 25% of a typical genome and are vital parts of many essential biological processes, structural knowledge of these proteins is necessary for increasing our understanding of such processes. Because structural knowledge of transmembrane proteins is difficult to attain experimentally, improved methods for prediction of structural features of these proteins are important.

Results: OCTOPUS, a new method for predicting transmembrane protein topology is presented and benchmarked using a dataset of 124 sequences with known structures. Using a novel combination of hidden Markov models and artificial neural networks, OCTOPUS predicts the correct topology for 94% of the sequences. In particular, OCTOPUS is the first topology predictor to fully integrate modeling of reentrant/membrane-dipping regions and transmembrane hairpins in the topological grammar.

Availability: OCTOPUS is available as a web server at http://octopus.cbr.su.se.

Contact: arne{at}bioinfo.se

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Burkhard Rost

Received on October 22, 2007; revised on May 1, 2008; accepted on May 3, 2008

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