Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces

BMC Systems Biology

Volumn 4, Issue SUPPL. 2, 2010, Pages

  Xia, Zheng ^a   Wu, Ling Yun ^b   Zhou, Xiaobo ^a   Wong, Stephen T C ^a  

^a WEILL CORNELL MEDICAL COLLEGE   (United States)

^b INSTITUTE OF APPLIED MATHEMATICS   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ARTIFICIAL INTELLIGENCE; DRUG DEVELOPMENT; DRUG INTERACTION; GENETIC DATABASE; HUMAN; HUMAN GENOME; PROTEIN ANALYSIS; SEQUENCE ANALYSIS; SYSTEM ANALYSIS; SYSTEMS BIOLOGY; VALIDATION STUDY;

ARTIFICIAL INTELLIGENCE; DATABASES, GENETIC; DRUG DISCOVERY; DRUG INTERACTIONS; GENOME, HUMAN; HUMANS; PROTEIN INTERACTION MAPPING; SEQUENCE ANALYSIS; SYSTEMS BIOLOGY; SYSTEMS INTEGRATION;

EID: 77956953029     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-4-6     Document Type: Article

References (18)

1. Yao L, Rzhetsky A. Quantitative systems-level determinants of human genes targeted by successful drugs. Genome Res 2008, 18(2):206-13. 10.1101/gr.6888208, 2203618, 18083776.
2. Keiser MJ, Roth BL, Armbruster BN, Ernsberger P, Irwin JJ, Shoichet BK. Relating protein pharmacology by ligand chemistry. Nat Biotechnol 2007, 25(2):197-206. 10.1038/nbt1284, 17287757.
3. Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, Hufeisen SJ, Jensen NH, Kuijer MB, Matos RC, Tran TB, Whaley R, Glennon RA, Hert J, Thomas KLH, Edwards DD, Shoichet BK, Roth BL. Predicting new molecular targets for known drugs. Nature 2009, 462(7270):175-181. 10.1038/nature08506, 2784146, 19881490.
4. Shoichet BK, McGovern SL, Wei B, Irwin JJ. Lead discovery using molecular docking. Curr Opin Chem Biol 2002, 6(4):439-46. 10.1016/S1367-5931(02)00339-3, 12133718.
5. Ballesteros J, Palczewski K. G protein-coupled receptor drug discovery: implications from the crystal structure of rhodopsin. Curr Opin Drug Discov Devel 2001, 4(5):561-74. 1383658, 12825452.
6. Jacob L, Vert JP. Protein-ligand interaction prediction: an improved chemogenomics approach. Bioinformatics 2008, 24(19):2149-56. 10.1093/bioinformatics/btn409, 2553441, 18676415.
7. Yamanishi Y, Araki M, Gutteridge A, Honda W, Kanehisa M. Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics 2008, 24(13):i232-40. 10.1093/bioinformatics/btn162, 2718640, 18586719.
8. Bleakley K, Yamanishi Y. Supervised prediction of drug-target interactions using bipartite local models. Bioinformatics 2009, 25(18):2397. 10.1093/bioinformatics/btp433, 2735674, 19605421.
9. Belkin M, Niyogi P, Sindhwani V. Manifold regularization: A geometric framework for learning from labeled and unlabeled examples. Journal of Machine Learning Research 2006, 7:2399-2434.
10. Sing T, Sander O, Beerenwinkel N, Lengauer T. ROCR: visualizing classifier performance in R. Bioinformatics 2005, 21(20):3940-1. 10.1093/bioinformatics/bti623, 16096348.
11. Yildirim MA, Goh KI, Cusick ME, Barabsi AL, Vidal M. Drug-target network. Nat Biotechnol 2007, 25(10):1119-1126. 10.1038/nbt1338, 17921997., http://dx.doi.org/10.1038/nbt1338
12. Yamanishi Y. Supervised bipartite graph inference. Proceedings of the Conference on Advances in Neural Information and Processing System 21:1433-1440.
13. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 2006, (34 Database):D354-7. 10.1093/nar/gkj102, 1347464, 16381885.
14. Wishart D, Knox C, Guo A, Shrivastava S, Hassanali M, Stothard P, Chang Z, Woolsey J. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Research 2006, (34 Database):D668. 10.1093/nar/gkj067, 1347430, 16381955.
15. Campillos M, Kuhn M, Gavin AC, Jensen LJ, Bork P. Drug target identification using side-effect similarity. Science 2008, 321(5886):263-6. 10.1126/science.1158140, 18621671.
16. Chapelle O, Schölkopf B, Zien A. Semi-supervised learning 2006, MIT press.
17. Hattori M, Okuno Y, Goto S, Kanehisa M. Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J Am Chem Soc 2003, 125(39):11853-65. 10.1021/ja036030u, 14505407.
18. Schölkopf B, Smola AJ. Learning with kernels 2002, MIT press Cambridge, Mass.