Update of TTD: Therapeutic Target Database

Nucleic Acids Research

Volumn 38, Issue SUPPL.1, 2009, Pages

  Zhu, Feng ^a   Han, BuCong ^a   Kumar, Pankaj ^a   Liu, XiangHui ^a   Ma, XiaoHua ^a   Wei, XiaoNa ^a   Huang, Lu ^a   Guo, YangFan ^a   Han, LianYi ^a   Zheng, ChanJuan ^a   Chen, YuZong ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; NEW DRUG; DRUG;

ACCESS TO INFORMATION; ARTICLE; BIOCHEMISTRY; CLINICAL TRIAL; COMPUTER PROGRAM; DRUG APPROVAL; DRUG INDICATION; DRUG INFORMATION; DRUG MECHANISM; DRUG RESEARCH; DRUG SCREENING; DRUG STRUCTURE; DRUG TARGETING; FOOD AND DRUG ADMINISTRATION; GENE SEQUENCE; HUMAN; INFORMATION PROCESSING; INTERNET; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; REFERENCE DATABASE; THERAPEUTIC TARGET DATABASE; BIOLOGY; CHEMISTRY; DRUG THERAPY; FACTUAL DATABASE; GENETIC DATABASE; INFORMATION RETRIEVAL; METHODOLOGY; PROTEIN DATABASE; UNITED STATES;

CHEMISTRY, PHARMACEUTICAL; CLINICAL TRIALS AS TOPIC; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; DATABASES, GENETIC; DATABASES, PROTEIN; DRUG APPROVAL; DRUG THERAPY; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; PHARMACEUTICAL PREPARATIONS; SOFTWARE; UNITED STATES; UNITED STATES FOOD AND DRUG ADMINISTRATION;

EID: 75549090848     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp1014     Document Type: Article

References (38)

1. Ohlstein, E.H., Ruffolo, R.R. Jr and Elliott, J.D. (2000) Drug discovery in the next millennium. Annu. Rev. Pharmacol. Toxicol., 40, 177-191.
2. Zambrowicz, B.P. and Sands, A.T. (2003) Knockouts model the 100 best-selling drugs-will they model the next 100? Nat. Rev. Drug Discov., 2, 38-51.
3. Zheng, C.J., Han, L.Y., Yap, C.W., Ji, Z.L., Cao, Z.W. and Chen, Y.Z. (2006) Therapeutic targets: progress of their exploration and investigation of their characteristics. Pharmacol Rev., 58, 259-279.
4. Golden, J.B. (2003) Prioritizing the human genome: knowledge management for drug discovery. Curr. Opin. Drug Discov. Dev., 6, 310-316.
5. Imming, P., Sinning, C. and Meyer, A. (2006) Drugs, their targets and the nature and number of drug targets. Nat. Rev. Drug Discov., 5, 821-834.
6. Overington, J.P., Al-Lazikani, B. and Hopkins, A.L. (2006) How many drug targets are there? Nat. Rev. Drug Discov., 5, 993-996.
7. Lindsay, M.A. (2003) Target discovery. Nat. Rev. Drug Discov., 2, 831-838.
8. Edwards, A. (2009) Large-scale structural biology of the human proteome. Annu. Rev. Biochem., 78, 541-568.
9. Lundstrom, K. (2006) Structural genomics: the ultimate approach for rational drug design. Mol. Biotechnol., 34, 205-212.
10. Kramer, R. and Cohen, D. (2004) Functional genomics to new drug targets. Nat. Rev. Drug Discov., 3, 965-972.
11. Dey, R., Khan, S. and Saha, B. (2007) A novel functional approach toward identifying definitive drug targets. Curr. Med. Chem., 14, 2380-2392.
12. Hopkins, A.L. (2008) Network pharmacology: the next paradigm in drug discovery. Nat. Chem. Biol., 4, 682-690.
13. Giallourakis, C., Henson, C., Reich, M., Xie, X. and Mootha, V.K. (2005) Disease gene discovery through integrative genomics. Annu. Rev. Genomics Hum. Genet., 6, 381-406.
14. Zimmermann, G.R., Lehar, J. and Keith, C.T. (2007) Multi-target therapeutics: when the whole is greater than the sum of the parts. Drug Discov. Today, 12, 34-42.
15. Jia, J., Zhu, F., Ma, X., Cao, Z., Li, Y. and Chen, Y.Z. (2009) Mechanisms of drug combinations: interaction and network perspectives. Nat. Rev. Drug Discov., 8, 111-128.
16. Liebler, D.C. and Guengerich, F.P. (2005) Elucidating mechanisms of drug-induced toxicity. Nat. Rev. Drug Discov., 4, 410-420.
17. Eichelbaum, M., Ingelman-Sundberg, M. and Evans, W.E. (2006) Pharmacogenomics and individualized drug therapy. Annu. Rev. Med., 57, 119-137.
18. Barcellos, G.B., Pauli, I., Caceres, R.A., Timmers, L.F., Dias, R. and de Azevedo, W.F. Jr (2008) Molecular modeling as a tool for drug discovery. Curr. Drug Targets, 9, 1084-1091.
19. Lee, G.M. and Craik, C.S. (2009) Trapping moving targets with small molecules. Science, 324, 213-215.
20. Zhu, F., Han, L., Zheng, C., Xie, B., Tammi, M.T., Yang, S., Wei, Y. and Chen, Y. (2009) What are next generation innovative therapeutic targets? Clues from genetic, structural, physicochemical, and systems profiles of successful targets. J. Pharmacol. Exp. Ther., 330, 304-315.
21. Han, L.Y., Zheng, C.J., Xie, B., Jia, J., Ma, X.H., Zhu, F., Lin, H.H., Chen, X. and Chen, Y.Z. (2007) Support vector machines approach for predicting druggable proteins: recent progress in its exploration and investigation of its usefulness. Drug Discov. Today, 12, 304-313.
22. Wishart, D.S., Knox, C., Guo, A.C., Cheng, D., Shrivastava, S., Tzur, D., Gautam, B. and Hassanali, M. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res., 36, D901-D906.
23. Gao, Z., Li, H., Zhang, H., Liu, X., Kang, L., Luo, X., Zhu, W., Chen, K., Wang, X. and Jiang, H. (2008) PDTD: a web-accessible protein database for drug target identification. BMC Bioinformatics, 9, 104.
24. Chen, X., Ji, Z.L. and Chen, Y.Z. (2002) TTD: Therapeutic Target Database. Nucleic Acids Res., 30, 412-415.
25. Yildirim, M.A., Goh, K.I., Cusick, M.E., Barabasi, A.L. and Vidal, M. (2007) Drug-target network. Nat. Biotechnol., 25, 1119-1126.
26. Wishart, D.S., Knox, C., Guo, A.C., Shrivastava, S., Hassanali, M., Stothard, P., Chang, Z. and Woolsey, J. (2006) DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res., 34, D668-D672.
27. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
28. Willett, P. (1998) Chemical similarity searching. J. Chem. Inf. Comput. Sci., 38, 983-996.
29. Ma, X.H., Wang, R., Yang, S.Y., Li, Z.R., Xue, Y., Wei, Y.C., Low, B.C. and Chen, Y.Z. (2008) Evaluation of virtual screening performance of support vector machines trained by sparsely distributed active compounds. J. Chem. Inf. Model, 48, 1227-1237.
30. George, R.A. and Heringa, J. (2002) Protein domain identification and improved sequence similarity searching using PSI-BLAST. Proteins, 48, 672-681.
31. Gerstein, M. (1998) Measurement of the effectiveness of transitive sequence comparison, through a third 'intermediate' sequence. Bioinformatics, 14, 707-714.
32. Wood, T.C. and Pearson, W.R. (1999) Evolution of protein sequences and structures. J. Mol. Biol., 291, 977-995.
33. Koehl, P. and Levitt, M. (2002) Sequence variations within protein families are linearly related to structural variations. J. Mol. Biol., 323, 551-562.
34. Li, Z.R., Han, L.Y., Xue, Y., Yap, C.W., Li, H., Jiang, L. and Chen, Y.Z. (2007) MODEL-molecular descriptor lab: a web-based server for computing structural and physicochemical features of compounds. Biotechnol. Bioeng., 97, 389-396.
35. Yap, C.W., Li, H., Ji, Z.L. and Chen, Y.Z. (2007) Regression methods for developing QSAR and QSPR models to predict compounds of specific pharmacodynamic, pharmacokinetic and toxicological properties. Mini Rev. Med. Chem., 7, 1097-1107.
36. Li, H., Yap, C.W., Ung, C.Y., Xue, Y., Li, Z.R., Han, L.Y., Lin, H.H. and Chen, Y.Z. (2007) Machine learning approaches for predicting compounds that interact with therapeutic and ADMET related proteins. J. Pharm. Sci., 96, 2838-2860.
37. Bostrom, J., Hogner, A. and Schmitt, S. (2006) Do structurally similar ligands bind in a similar fashion? J. Med. Chem., 49, 6716-6725.
38. Huang, N., Shoichet, B.K. and Irwin, J.J. (2006) Benchmarking sets for molecular docking. J. Med. Chem., 49, 6789-6801.