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Bioinformatics. 2005 Nov 15;21(22):4101-6. Epub 2005 Sep 20.

Prediction of the coupling specificity of GPCRs to four families of G-proteins using hidden Markov models and artificial neural networks.

Author information

  • 1Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Greece.

Abstract

MOTIVATION:

G-protein coupled receptors are a major class of eukaryotic cell-surface receptors. A very important aspect of their function is the specific interaction (coupling) with members of four G-protein families. A single GPCR may interact with members of more than one G-protein families (promiscuous coupling). To date all published methods that predict the coupling specificity of GPCRs are restricted to three main coupling groups G(i/o), G(q/11) and G(s), not including G(12/13)-coupled or other promiscuous receptors.

RESULTS:

We present a method that combines hidden Markov models and a feed-forward artificial neural network to overcome these limitations, while producing the most accurate predictions currently available. Using an up-to-date curated dataset, our method yields a 94% correct classification rate in a 5-fold cross-validation test. The method predicts also promiscuous coupling preferences, including coupling to G(12/13), whereas unlike other methods avoids overpredictions (false positives) when non-GPCR sequences are encountered.

AVAILABILITY:

A webserver for academic users is available at http://bioinformatics.biol.uoa.gr/PRED-COUPLE2

PMID:
16174684
[PubMed - indexed for MEDLINE]
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