Bioinformatics Advance Access originally published online on July 15, 2009
Bioinformatics 2009 25(18):2397-2403; doi:10.1093/bioinformatics/btp433
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Supervised prediction of drug–target interactions using bipartite local models
1Mines ParisTech, Centre for Computational Biology, 35 rue Saint-Honoré, F-77305 Fontainebleau Cedex, 2Institut Curie and 3INSERM, U900, F-75248, Paris, France
*To whom correspondence should be addressed.
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Abstract |
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Motivation: In silico prediction of drug–target interactions from heterogeneous biological data is critical in the search for drugs for known diseases. This problem is currently being attacked from many different points of view, a strong indication of its current importance. Precisely, being able to predict new drug–target interactions with both high precision and accuracy is the holy grail, a fundamental requirement for in silico methods to be useful in a biological setting. This, however, remains extremely challenging due to, amongst other things, the rarity of known drug–target interactions.
Results: We propose a novel supervised inference method to predict unknown drug–target interactions, represented as a bipartite graph. We use this method, known as bipartite local models to first predict target proteins of a given drug, then to predict drugs targeting a given protein. This gives two independent predictions for each putative drug–target interaction, which we show can be combined to give a definitive prediction for each interaction. We demonstrate the excellent performance of the proposed method in the prediction of four classes of drug–target interaction networks involving enzymes, ion channels, G protein-coupled receptors (GPCRs) and nuclear receptors in human. This enables us to suggest a number of new potential drug–target interactions.
Availability: An implementation of the proposed algorithm is available upon request from the authors. Datasets and all prediction results are available at http://cbio.ensmp.fr/~yyamanishi/bipartitelocal/.
Contact: kevbleakley{at}gmail.com
Supplementary information: Supplementary data are available at Bioinformatics online.
Associate Editor: Olga Troyanskaya
Received on March 17, 2009; revised on June 12, 2009; accepted on July 7, 2009
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