Target, chemical and bioactivity databases - integration is key

Drug Discovery Today: Technologies

Volumn 3, Issue 4, 2006, Pages 357-365

  Oprea, Tudor I ^a   Tropsha, Alexander ^b  

^a UNIVERSITY OF NEW MEXICO SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DRUG;

ACCESS TO INFORMATION; BIBLIOGRAPHIC DATABASE; BIOASSAY; BIOINFORMATICS; BIOLOGY; CHEMICAL ANALYSIS; CHEMICAL STRUCTURE; COMBINATORIAL CHEMISTRY; CYTOLOGY; DRUG ACTIVITY; DRUG INDUSTRY; DRUG RESEARCH; DRUG TARGETING; GENETICS; INFORMATION PROCESSING; INTERNET; MOLECULAR BIOLOGY; REVIEW; SCIENTIFIC LITERATURE; TOXICOLOGY;

EID: 33846538483     PISSN: 17406749     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ddtec.2006.12.003     Document Type: Review

References (31)

1. Olah M., and Oprea T.I. Bioactivity databases. In: Taylor J.B., and Triggle D.J. (Eds). Comprehensive Medicinal Chemistry II Vol. 3 (2006), Elsevier, Oxford 293-313
2. Wisniewski J.L. Chemical nomenclature and structure representation: algorithmic generation and conversion. In: Gasteiger J. (Ed). Handbook of Cheminformatics Vol. 2 (2003), Wiley-VCH, Weinheim 51-79
3. Fisanick W., and Shively E.R. The CAS information system: applying scientific knowledge and technology for better information. In: Gasteiger J. (Ed). Handbook of Cheminformatics Vol. 2 (2003), Wiley-VCH, Weinheim 556-607
4. Olah M., et al. WOMBAT: world of molecular bioactivity. In: Oprea T.I. (Ed). Chemoinformatics in Drug Discovery Vol. 23 (2005), Wiley-VCH, Weinheim 223-239
5. Neubig R.R., et al. International Union of Pharmacology Committee on Receptor Nomenclature and Drug Classification. XXXVIII. Update on terms and symbols in quantitative pharmacology. Pharmacol. Rev. 55 (2003) 597-606
6. Oprea T.I., et al. Rapid ADME filters for lead discovery. In: Cruciani G. (Ed). Molecular Interaction Fields Vol. 24 (2005), Wiley-VCH, Weinheim 249-272
7. Horn F., et al. Collecting and harvesting biological data: the GPCRDB and NucleaRDB information systems. Nucleic Acids Res. 29 (2001) 346-349. http://www.receptors.org/NR/ (http://www.receptors.org/NR/)
8. Horn F., et al. GPCRDB: an information system for G protein-coupled receptors. Nucleic Acids Res. 26 (1998) 275-279. http://www.gpcr.org/7tm/ (http://www.gpcr.org/7tm/)
9. Bright M.W., et al. A taxonomy and current issues in multidatabase systems. Computer 25 (1992) 50-60
10. Larson J.A. Database Directions: From Relational to Distributed, Multimedia, and Object-Oriented Database Systems (1995), Prentice-Hall PTR, New Jersey pp. 45-56
11. Siegel J. CORBA Fundamentals and Programming (1996), John Wiley & Sons, Inc., New York
12. Powell T.A. HTML: The Complete Reference. 2nd edn (1999), Osborne/McGraw-Hill, Berkeley
13. Berman H.M., et al. The protein data bank. Nucleic Acids Res. 28 (2000) 235-242. http://www.rcsb.org/pdb/ (http://www.rcsb.org/pdb/)
14. Austin C.P., et al. NIH molecular libraries initiative (Austin et al., 2004). Science 306 (2004) 1138-1139. http://nihroadmap.nih.gov/ (http://nihroadmap.nih.gov/)
15. Lipinski C.A., et al. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 23 (1997) 3-25
16. Wishart D.S., et al. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 34 Database issue (2006) D668-D672
17. Roth B.L., et al. The multiplicity of serotonin receptors: uselessly diverse molecules or an embarrassment of riches?. Neuroscientist 6 (2000) 252-262
18. Chen X., et al. TTD: therapeutic target database. Nucleic Acids Res. 30 (2002) 412-415
19. Ji Z.L., et al. Drug adverse reaction target database (DART): proteins related to adverse drug reactions. Drug Saf. 26 (2003) 685-690
20. Sun L.Z., et al. Absorption, distribution, metabolism, and excretion-associated protein database. Clin. Pharmacol. Ther. 71 (2002) 405-416
21. Zheng C.J., et al. TRMP: a database of therapeutically relevant multiple pathways. Bioinformatics 20 (2004) 2236-2241
22. Chen X., et al. CLiBE: a database of computed ligand binding energy for ligand-receptor complexes. Comp. Chem. 26 (2002) 661-666
23. Ji Z.L., et al. KDBI: kinetic data of bio-molecular interactions database. Nucleic Acids Res. 31 (2003) 255-257
24. Alfarano C., et al. The biomolecular interaction network database and related tools 2005 update. Nucleic Acids Res. 33 Database issue (2005) D418-D424. http://bind.ca/ (http://bind.ca/)
25. Benson D.A., et al. GenBank: update. Nucleic Acids Res. 32 Database issue (2004) D23-D26. http://www.ncbi.nih.gov/Genbank/ (http://www.ncbi.nih.gov/Genbank/)
26. Aizawa M., et al. KiBank: a database for computer-aided drug design based on protein-chemical interaction analysis. Yakugaku Zasshi: J. Pharm. Soc. Jpn. 124 (2004) 613-619
27. Zhang J.-W., et al. Development of KiBank, a database supporting structure-based drug design. Comput. Biol. Chem. 28 (2004) 401-407
28. Irwin J.J., et al. ZINC - a free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 45 (2005) 177-182
29. Oprea T.I., et al. Integrating virtual screening in lead discovery. Curr. Opin. Chem. Biol. 8 (2004) 349-358
30. Cases M., et al. Chemical and biological profiling of an annotated compound library directed to the nuclear receptor family. Curr. Top. Med. Chem. 5 (2005) 763-772
31. Savchuck N.P., et al. Exploring the chemogenomic knowledge space with annotated chemical libraries. Curr. Opin. Chem. Biol. 8 (2004) 412-417