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In the drug discovery process high-throughput screening is often applied as initial procedure for the identification of hit molecules against a certain target, e.g. an enzyme or G protein-coupled receptor. In addition, virtual screening campaigns utilizing commercially available compound libraries are often performed that allow the search for potential hit molecules within a much larger chemical space as usually accessible within the in-house compound libraries. Chemoinformatic tools provide the opportunity to assist in the setup of experimental and virtual screening campaigns (e.g. assembly of compound libraries) as well as the analysis of screening results and structures of hit compounds. In this presentation the implementation of ChemAxon tools into the European ScreeningPort workflow will be presented using selected examples from previous and ongoing experimental and virtual screening campaigns.