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Pre-clinical drug discovery strategies include target-based and phenotypic screening, natural substance modifications and biologic approaches. To demonstrate how cheminformatics approaches contributed to the discovery of new medicines we analysed recently approved drugs. In this presentations, we place ChemAxon’s Discovery toolkit in this context and demonstrate possible applications for 2D and 3D similarity studies, high-throughput pairwise molecular alignments or scaffold hopping. Moreover, we also discuss the technological challenges and realization of such applications in corporate platforms.