Bioactivity databases

Oprea, T., Tropsha, A. (2006) Target, chemical and bioactivity databases - integration is key. Drug Discov Today 3, 357-365. 

WOMBAT and WOMBAT-PK Bioactivity Databases for Lead and Drug Discovery... 

Because the internal dissemination of this database within AstraZeneca R D (a company with 11 R D sites across four continents) was not deemed a success, AstraZeneca decided to discontinue the project as of May 2002. Backed by private funding, the database, renamed WOrld of Molecular BioAc-Tivity (WOMBAT) in 2003, continued to evolve [13] as discussed for WOMBAT 2006.1, below. Recognizing the paucity of chemical databases that capture clinical pharmacokinetics data in a searchable manner, we further developed the WOMBAT-PK (WOMBAT-Pharmacokinetics), to index such data from literature [14]. This chapter summarizes the contents of WOMBAT and WOMBAT-PK [15], some of the problems encountered in appropriately indexing biological activities and correct chemical structures (with focus on machine-readable contents for data mining), and provides some examples of data mining with WOMBAT. Other bioactivity databases [16], focused mostly on patent literature, are shown in Table 13.2-1 together with the on-line references. 

M. Olah, T.I. Oprea, Bioactivity databases, in Comprehensive Medicinal Chemistry II, (Eds. J. Taylor,... 

Olah, M., Oprea, T.I. Bioactivity Databases. In Triggle, D., Taylor, editors. Comprehensive Medicinal Chemistry II, vol. 3. Oxford Elsevier 2006, pp. 293-313. 

Of the recently developed formalisms reminiscent to Bioster analogue pairs, the somatched molecular pair (MMP) [28] rehes on strictly defined compound pairs that differ only by just one atom or small atomic group. Applying MMP methodology to sets of analogue series retrieved by systematic searching from publicly available bioactivity databases, several common and uncommon bioisosteric replacement pairs could be identified [29]. 

Gaulton, A.. Beilis. L.J.. Bento. A.P.. Chambers,)., Davies, M., Hersey, A., Light, Y., McGlinchey, S., Michalovich, D., Al-Lazikani, B., and Overington, J.P. (2011) ChEMBL a large-scale bioactivity database for drug discovery. Nucleic Acids Research, 40, 1-8. 

Bento, A.P., Gaulton, A., Hersey, A. et al (2014) The ChEMBL bioactivity database an update. Nucleic Acids Research, 42, 1083-1090. 

Olah, M., Rad, R., Ostopovici, L., Bora, A., Hadaruga, N., Hadaruga, D., et al. (2007). WOMBAT and WOMBAT-PK Bioactivity databases for lead and drug discovery. In S. L. Schreiber, T. M. Kapoor, G. Weiss (Eds.), Chemical biology From small molecules to systems biology and drug design (pp. 760-786). Weinheim Wiley-VCH. 

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