{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T11:23:32Z","timestamp":1772191412879,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2315,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: \u00a0In silico prediction of drug\u2013target interactions from heterogeneous biological data is critical in the search for drugs and therapeutic targets for known diseases such as cancers. There is therefore a strong incentive to develop new methods capable of detecting these potential drug\u2013target interactions efficiently.<\/jats:p>\n               <jats:p>Results: In this article, we investigate the relationship between the chemical space, the pharmacological space and the topology of drug\u2013target interaction networks, and show that drug\u2013target interactions are more correlated with pharmacological effect similarity than with chemical structure similarity. We then develop a new method to predict unknown drug\u2013target interactions from chemical, genomic and pharmacological data on a large scale. The proposed method consists of two steps: (i) prediction of pharmacological effects from chemical structures of given compounds and (ii) inference of unknown drug\u2013target interactions based on the pharmacological effect similarity in the framework of supervised bipartite graph inference. The originality of the proposed method lies in the prediction of potential pharmacological similarity for any drug candidate compounds and in the integration of chemical, genomic and pharmacological data in a unified framework. In the results, we make predictions for four classes of important drug\u2013target interactions involving enzymes, ion channels, GPCRs and nuclear receptors. Our comprehensively predicted drug\u2013target interaction networks enable us to suggest many potential drug\u2013target interactions and to increase research productivity toward genomic drug discovery.<\/jats:p>\n               <jats:p>Supplementary information: Datasets and all prediction results are available at http:\/\/cbio.ensmp.fr\/~yyamanishi\/pharmaco\/.<\/jats:p>\n               <jats:p>Availability: Softwares are available upon request.<\/jats:p>\n               <jats:p>Contact: \u00a0yoshihiro.yamanishi@ensmp.fr<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq176","type":"journal-article","created":{"date-parts":[[2010,6,7]],"date-time":"2010-06-07T07:28:13Z","timestamp":1275895693000},"page":"i246-i254","source":"Crossref","is-referenced-by-count":410,"title":["Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework"],"prefix":"10.1093","volume":"26","author":[{"given":"Yoshihiro","family":"Yamanishi","sequence":"first","affiliation":[{"name":"1 Mines ParisTech, Centre for Computational Biology, 35 rue Saint-Honore, F-77305 Fontainebleau Cedex, 2 Institut Curie, F-75248, 3 INSERM U900, F-75248, Paris, France, 4 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 and 5 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai Minato-ku, Tokyo 108-8639, Japan"},{"name":"1 Mines ParisTech, Centre for Computational Biology, 35 rue Saint-Honore, F-77305 Fontainebleau Cedex, 2 Institut Curie, F-75248, 3 INSERM U900, F-75248, Paris, France, 4 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 and 5 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai Minato-ku, Tokyo 108-8639, Japan"},{"name":"1 Mines ParisTech, Centre for Computational Biology, 35 rue Saint-Honore, F-77305 Fontainebleau Cedex, 2 Institut Curie, F-75248, 3 INSERM U900, F-75248, Paris, France, 4 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 and 5 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai Minato-ku, Tokyo 108-8639, Japan"}]},{"given":"Masaaki","family":"Kotera","sequence":"additional","affiliation":[{"name":"1 Mines ParisTech, Centre for Computational Biology, 35 rue Saint-Honore, F-77305 Fontainebleau Cedex, 2 Institut Curie, F-75248, 3 INSERM U900, F-75248, Paris, France, 4 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 and 5 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai Minato-ku, Tokyo 108-8639, Japan"}]},{"given":"Minoru","family":"Kanehisa","sequence":"additional","affiliation":[{"name":"1 Mines ParisTech, Centre for Computational Biology, 35 rue Saint-Honore, F-77305 Fontainebleau Cedex, 2 Institut Curie, F-75248, 3 INSERM U900, F-75248, Paris, France, 4 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 and 5 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai Minato-ku, Tokyo 108-8639, Japan"},{"name":"1 Mines ParisTech, Centre for Computational Biology, 35 rue Saint-Honore, F-77305 Fontainebleau Cedex, 2 Institut Curie, F-75248, 3 INSERM U900, F-75248, Paris, France, 4 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 and 5 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai Minato-ku, Tokyo 108-8639, Japan"}]},{"given":"Susumu","family":"Goto","sequence":"additional","affiliation":[{"name":"1 Mines ParisTech, Centre for Computational Biology, 35 rue Saint-Honore, F-77305 Fontainebleau Cedex, 2 Institut Curie, F-75248, 3 INSERM U900, F-75248, Paris, France, 4 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011 and 5 Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai Minato-ku, Tokyo 108-8639, Japan"}]}],"member":"286","published-online":{"date-parts":[[2010,6,1]]},"reference":[{"key":"2023012508070015400_B1","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1124\/jpet.102.042853","article-title":"Inhibition of prostaglandin h2 synthases by salicylate is dependent on the oxidative state of the enzymes","volume":"304","author":"Aronoff","year":"2003","journal-title":"J. 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