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BioMed Research International
Volume 2015, Article ID 350983, 9 pages
http://dx.doi.org/10.1155/2015/350983
Research Article

Predicting Drug-Target Interactions via Within-Score and Between-Score

1School of Life Sciences, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
2School of Computer Science, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China

Received 19 November 2014; Accepted 6 January 2015

Academic Editor: Liam McGuffin

Copyright © 2015 Jian-Yu Shi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. M. R. Hurle, L. Yang, Q. Xie, D. K. Rajpal, P. Sanseau, and P. Agarwal, “Computational drug repositioning: from data to therapeutics,” Clinical Pharmacology & Therapeutics, vol. 93, no. 4, pp. 335–341, 2013. View at Publisher · View at Google Scholar · View at Scopus
  2. M. Kanehisa, M. Araki, S. Goto et al., “KEGG for linking genomes to life and the environment,” Nucleic Acids Research, vol. 36, supplement 1, pp. D480–D484, 2008. View at Publisher · View at Google Scholar · View at Scopus
  3. E. E. Bolton, Y. Wang, P. A. Thiessen, and S. H. Bryant, “PubChem: integrated platform of small molecules and biological activities,” Annual Reports in Computational Chemistry, vol. 4, pp. 217–241, 2008. View at Publisher · View at Google Scholar
  4. V. Law, C. Knox, Y. Djoumbou et al., “DrugBank 4.0: shedding new light on drug metabolism,” Nucleic Acids Research, vol. 42, no. 1, pp. D1091–D1097, 2014. View at Publisher · View at Google Scholar · View at Scopus
  5. A. Gaulton, L. J. Bellis, A. P. Bento et al., “ChEMBL: a large-scale bioactivity database for drug discovery,” Nucleic Acids Research, vol. 40, no. D1, pp. D1100–D1107, 2012. View at Publisher · View at Google Scholar · View at Scopus
  6. M. A. Yildirim, K.-I. Goh, M. E. Cusick, A.-L. Barabási, and M. Vidal, “Drug—target network,” Nature Biotechnology, vol. 25, no. 10, pp. 1119–1126, 2007. View at Publisher · View at Google Scholar · View at Scopus
  7. F. Cheng, C. Liu, J. Jiang et al., “Prediction of drug-target interactions and drug repositioning via network-based inference,” PLoS Computational Biology, vol. 8, no. 5, Article ID e1002503, 2012. View at Publisher · View at Google Scholar · View at Scopus
  8. K. Bleakley and Y. Yamanishi, “Supervised prediction of drug-target interactions using bipartite local models,” Bioinformatics, vol. 25, no. 18, pp. 2397–2403, 2009. View at Publisher · View at Google Scholar · View at Scopus
  9. T. van Laarhoven, S. B. Nabuurs, and E. Marchiori, “Gaussian interaction profile kernels for predicting drug-target interaction,” Bioinformatics, vol. 27, no. 21, pp. 3036–3043, 2011. View at Publisher · View at Google Scholar · View at Scopus
  10. J.-P. Mei, C.-K. Kwoh, P. Yang, X.-L. Li, and J. Zheng, “Drug-target interaction prediction by learning from local information and neighbors,” Bioinformatics, vol. 29, no. 2, pp. 238–245, 2013. View at Publisher · View at Google Scholar · View at Scopus
  11. T. Klabunde, “Chemogenomic approaches to drug discovery: similar receptors bind similar ligands,” British Journal of Pharmacology, vol. 152, no. 1, pp. 5–7, 2007. View at Publisher · View at Google Scholar · View at Scopus
  12. F. J. Azuaje, L. Zhang, Y. Devaux, and D. R. Wagner, “Drug-target network in myocardial infarction reveals multiple side effects of unrelated drugs,” Scientific Reports, vol. 1, article 52, 2011. View at Publisher · View at Google Scholar · View at Scopus
  13. Y. Yamanishi, M. Araki, A. Gutteridge, W. Honda, and M. Kanehisa, “Prediction of drug-target interaction networks from the integration of chemical and genomic spaces,” Bioinformatics, vol. 24, no. 13, pp. i232–i240, 2008. View at Publisher · View at Google Scholar · View at Scopus
  14. M. Hattori, Y. Okuno, S. Goto, and M. Kanehisa, “Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways,” Journal of the American Chemical Society, vol. 125, no. 39, pp. 11853–11865, 2003. View at Publisher · View at Google Scholar · View at Scopus
  15. T. F. Smith and M. S. Waterman, “Identification of common molecular subsequences,” Journal of Molecular Biology, vol. 147, no. 1, pp. 195–197, 1981. View at Publisher · View at Google Scholar · View at Scopus
  16. J. I. F. Bass, A. Diallo, J. Nelson, J. M. Soto, C. L. Myers, and A. J. M. Walhout, “Using networks to measure similarity between genes: association index selection,” Nature Methods, vol. 10, no. 12, pp. 1169–1176, 2013. View at Publisher · View at Google Scholar · View at Scopus
  17. J. Davis and M. Goadrich, “The relationship between Precision-Recall and ROC curves,” in Proceedings of the 23rd International Conference on Machine Learning (ICML '06), ACM, 2006.