Virtual databases

The average error in the external prediction was about +0.8 log unit. Although this range was still not suitable to predict the precise solubility values of external compounds, it was sufficient to rank compounds in different solubility categories and to use it for the filtering of compounds in virtual databases. 

These results were used to screen a virtual database of primary amine fragments to enhance binding affinity in the P3 pocket using a related scaffold as shown in Figure 9.15. The virtual screening was quickly accomplished through Merck s in-house web-based tools described in Section 9.6 and was in fact a test of these tools. 

Data mining of chemical databases is still at its very early stage. Nevertheless, as a result of the data explosion in pharmaceutical industry, it is expected that data mining techniques will play an increasingly important role in the drug discovery process. Future studies may include, for example, the definition of chemical space, the validation of various algorithms (206), and the representation of extremely large virtual databases (207). 

Avigdor G (2005) On the cardinality of schema matching. In OTM workshops, pp 947-956 Berlin J, Motro A (2001) Automated discovery of contents for virtual databases. In CoopIS. Springer, Heidelberg, pp 108-122... 

IBM s DiscoveryLink uses database middleware technology to provide integrated access to biological data sources. DiscoveryLink provides users with a virtual database to which they can pose arbitrarily complex queries in the high-level, nonprocedural query language SQL. 

In a compound collection enhancement strategy, only very few of the possible structures are eventually produced. Some companies have also generated large virtual databases based on validated reaction protocols, such as Pfizer s Q>Libri with over 10 members [28]. Enamine [29], a Ukrainian provider of test compoimds, has a virtual library with 30 million compoimds based on their experience of a well-performing reaction combined with a large number of available diversity reagents, called the fiill real database. ... 

MDMS-SL analyzes lipid molecular species in a combined targeted and nontargeted approach and extensively employs the building-block concept for identification of lipid molecular structures (see Chapter 2). The database for MDMS-SL should be as broad and flexible as possible and can be readily constructed based on the building blocks of individual lipid classes (see Chapter 1) [3]. Such a virtual database consists... 

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