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In 2012, 26 of the 39 new therapeutic products approved by the FDA, two thirds of the total, were small molecule drugs indicating that medicinal chemistry is still the forefront of drug discovery R&D. Despite this, drug discovery chemistry is a multi-tiered problem: from identifying a therapeutic MOA, to making unique and defensible chemistry, to SAR and pharmacophore modeling, to understanding pharmacokinetic properties, bioavailability and safety. Each aspect builds on the rest because it is not just about making a unique and therapeutically active compound; it is also about being able to deliver it effectively and safely within patients. The following presentations highlight various aspects of how ChemAxon’s products and tools can be used in drug discovery chemistry; from reaction mapping, property calculation, structure filtering and virtual screening to metabolite prediction, chemistry text analytics and knowledge management and as well as our recent advances in biomolecular structure management.