PubChem molecular similarity

These are some examples of the analysis that can be performed for three representative datasets in Table 2.2. Similar analysis using these or other molecular representations can be conducted for other databases. In fact, a comparison of the collection of drugs analyzed here with natural products and compounds obtained from PubChem has been published elsewhere (Singh et ah, 2009). 

Cincilla, G., Thormarm, M., and Pons, M. (2010) Structuring chemical space similarity-based characterization of the PubChem database. Molecular Informatics, 29, 37 9. 

A number of food phytochemicals and food-related molecular databases are available [21], Food and food-related databases are described in more detail in Chap. 9 of this book. Major examples of public databases of chemical compounds annotated with biological activity for dmg-discoveiy apphcations have been developed. Prominent examples include BindingDB, ChEMBL, PubChem, and WOrld of Molecular BioAcTivity (WOMBAT). These databases and others described in Chap. 9 can be analyzed and compared for knowledge of chemical space coverage and potential repurposing, for example, using the concept of similarity searching. 

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