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Cytochrome P450 enzymes (CYPs) metabolize the majority of small molecule drug compounds. They catalyze a wide variety of chemical reactions, and potentially, a large number of different metabolites can be generated. Due to the promiscuous nature of the CYPs, it is not trivial to predict what metabolites are generated. It is, however, important to know where a compound is metabolized and which metabolites are formed. This gives the possibility to redesign the compound if it is too rapidly metabolized or to avoid the formation of toxic metabolites. These questions are important both for understanding the action of known drugs (including drug–drug interactions, an important issue in adverse drug reactions) and for the development of new and/or improved drugs. In this chapter we will discuss in silico methods for prediction of the sites of metabolism with an emphasis on how the compounds bind and how easily a site in the compounds reacts with the enzyme.

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