WOMBAT database

II. Products Summary Daylight provides chemoinformatics tools and databases for life sciences. Daylight s product portfolio includes DayCart, THOR database, Merlin exploratory data analysis, ACD database, MedChem database, SPRESI database, WOMBAT database, World Drug Index database. 

Jenkins et alP have used ligand activity data from the well-curated WOMBAT database to build a series of 2D models to predict the most likely protein targets for... 

The WOMBAT database schemata, illustrated in Fig. 13.2-3, are further discussed in the next section. Their organization, illustrated in Figs. 13.2-4 to 13.2-6, shows the 3 panels of the database The Bioactivity Summary... 

In an effort to understand if HAMs are, in any way, different from LAMs (low activity molecules), we extended this survey to compounds published between 1991 and 2002, as indexed in WOMBAT [26]. This database [27] contains 4927 unique structures with at least one measured activity better than 1 nM (HAMs), and 34028 unique structures with at least one activity less than 1 XM (LAMs). Between HAMs and LAMs, 1080 molecules are common, that is, they have at least one activity above 1 nM and at least one activity below 1 XM. This is not uncommon for, for example, highly selective molecules. We did not exclude these from either set since we monitor trends, not exact figures. We studied these trends using 2-D-(two-dimensional) descriptors, that is, descriptors that do not use information related to the three-dimensional characteristics of model compounds. These descriptors can be classified as follows ... 

I 9 WOMBAT World of Molecular Bioactivity Tab. 9.1 Examples of annotated databases... 

Fig. 9.1 Bioactivity distribution pie charts in WOMBAT 2004.1, classified by target type. The size of the pie chart is proportional to the representation of each target class in the database.

Being an annotated database, WOMBAT continues to evolve in time - not only with the addition of more entries but also with updates and restructuring of the biological and chemical information, which is subject to change even after the data is captured. The... 

WOMBAT [39] is a Cabinet database that provides information about biological activity of small molecules [40]. The dataset comes from publications in the Journal of Medicinal Chemistry and other periodicals. WOMBAT is updated twice a year. The data consist of series of compounds that were observed and compared for a specific activity, for example, Ki, IC50, D2 and EC50. The database also includes calculated LogP and Log S values, as well as other descriptors related to flexibility, size, and so on. 

Each substance in the database has its unique ID number. With every structure, there are two associated functions similar and related. Similar searches WOMBAT and related searches all Cabinet databases. Some series involve an enzyme with an EC number listed and can be searched by selecting the related by EC button. 

When the related button above the structure is selected, a list of similar structures in other databases is shown. Empath, Planet, TCM and WOMBAT are found. In Planet, the closest structure is IHWK. Selecting it brings up the Planet version of the PDB... 

Based on 450 drugs with qualitative BBB data from WOMBAT-PK, we find that 83 /o of molecules with (N+0)<5 and only 30 /o of molecules with (N + 0) >5 were annotated in the database as passing the blood-brain barrier. The percentage of drugs passing the barrier linearly decreased with sum of (N + 0) atoms up to 6 atoms followed by drastic decrease in percentage of... 

WOMBAT Literature Data and 14 Patent families from MDL Patent Database FCFP4 similarity search(675) and NB model (5000)... 

Examples of other freely or commercially available annotated chemogenomics databases include WOMBAT, REGG, and DmjjBank. Note, however, that SEA can be used with any kind of annotation and is not limited to ligand-target association. 

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. 

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