FreeFlowDB: Storage, Querying and Interacting with Structure-Activity Information from High-Throughput Drug Discovery

The state of the art in modern drug discovery involves investigating a large number of drug-like molecules using medium or high-throughput assays, often being conducted against multiple targets. Managing the information generated in such processes requires the ability to deal ´with complex, multifarious data as well, as the development of new user-data interaction paradigms that help glean patterns hidden in the multitude of data by emphasizing exploration and information assimilation. This paper describes our research in developing FreeFlowDB, a drug discovery information database system that is geared towards storing both structural as well as high-throughput assay information generated as part of a typical drug discovery process. FreeFlowDB supports powerful structural querying facilities that subsume within a common algorithmic framework exact structural matching, sub-structure querying, and in-exact matching. Furthermore, the system supports unified visualization-query facilities that allow interacting with assay as well as structure-activity information. This allows efficacious and intuitive query-analysis of large, amounts of data for knowledge discovery. Case studies and experimental results demonstrate the capabilities of the system