Chemogenomics defines the screening of a chemical universe, i.e. all possible chemical compounds, against a target universe, in this case all proteins and their potential drug targets. Target-based chemogenomics approaches are intended to be used for any kind of target family, provided that a multiple alignment of all targets to compare is reachable. The dual approaches of chemogenomics promises to add a fresh influx of knowledge in cheminformatics, gene discovery, gene regulation and molecular signalling and hence give hope for finding novel therapeutics against disorders like cancers. Predicting interactions between small molecules and proteins is a crucial step towards deciphering many biological processes, and plays a critical role in drug discovery. It offers hope to resolve the ethical issues regarding stem cells by providing a safe and practical method of stem cell regeneration.