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Bioinformatics Advance Access originally published online on September 10, 2009
Bioinformatics 2009 25(21):2757-2763; doi:10.1093/bioinformatics/btp539
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information

Lisa Bartoli 1, Piero Fariselli 1,*, Anders Krogh 2 and Rita Casadio 1

1 Biocomputing Group, Department of Biology, University of Bologna, Via Irnerio 42, 40126, Bologna, Italy and 2 The Bioinformatics Center, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark

* To whom correspondence should be addressed.


  Abstract

Motivation:The widespread coiled-coil structural motif in proteins is known to mediate a variety of biological interactions. Recognizing a coiled-coil containing sequence and locating its coiled-coil domains are key steps towards the determination of the protein structure and function. Different tools are available for predicting coiled-coil domains in protein sequences, including those based on position-specific score matrices and machine learning methods.

Results: In this article, we introduce a hidden Markov model (CCHMM_PROF) that exploits the information contained in multiple sequence alignments (profiles) to predict coiled-coil regions. The new method discriminates coiled-coil sequences with an accuracy of 97% and achieves a true positive rate of 79% with only 1% of false positives. Furthermore, when predicting the location of coiled-coil segments in protein sequences, the method reaches an accuracy of 80% at the residue level and a best per-segment and per-protein efficiency of 81% and 80%, respectively. The results indicate that CCHMM_PROF outperforms all the existing tools and can be adopted for large-scale genome annotation.

Availability: The dataset is available at http://www.biocomp.unibo.it/~lisa/coiled-coils. The predictor is freely available at http://gpcr.biocomp.unibo.it/cgi/predictors/cchmmprof/pred_cchmmprof.cgi.

Contact: piero{at}biocomp.unibo.it

Associate Editor: Anna Tramontano

Received on May 12, 2009; revised on August 20, 2009; accepted on August 23, 2009

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