Target prediction, database

The following section outlines the more detailed requirements of databases used in target prediction for safety pharmacology. Also, Table 13.2 provides an overview of currently available databases and how far they reach the desired standard. 

Table 13.2 An overview of databases amenable for target prediction.

Noncomprehensive list of tools and databases for predicting metabolic fate, linking chemical structures to biological targets, and performing functional analysis of molecular targets... 

Fig. 5. Subset of possible targets for clozapine (only targets classed as enzymes are shown) showing the predicted target, the database compound driving the prediction, the Tanimoto coefficient percentage of its similarity to the query compound (in this case clozapine was found in the database, hence similarity score is 100%), the effect on the target (where known) and the PubMed ID or patent ID from which the compound-target association was drawn. Targets predicted by QSAR models are also indicated.

J., Bond, P.J., Whitmore, A.V., Zimmer, S., Young, M.P., Jenkins, J.L., Glick, M., Glen, R.C., and Bender, A. (2011) From in silico target prediction to multi-target drug design current databases, methods and applications. /. Proteomics, 74, 2554-2574. 

Virtual screening uses computational docking methods to assess which of a large database of compounds will fit into the unliganded structure of the target protein. Current protocols and methods can, with up to 80% success, predict the binding position and orientation of ligands that are known to bind... 

Threading essentially entails comparing the sequence of the polypeptide whose three-dimensional structure you wish to predict with the database sequences known to generate specific fold patterns. Computer programs can then be used to estimate the probability of the target sequence adopting each known folding structure. 

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