This contribution aims for a brief, but as comprehensive as possible, overview of computational enzymology examining all the steps necessary for an enzyme (enzyme–substrate complex formation, chemical reaction, product release and catalytic cycle restoration) to exert its catalytic action. Due to its great importance in pharmacology, covalent inhibition is also considered. Examples of how to extract valuable information from the combined use of classical molecular dynamics with pure and hybrid quantum chemical tools (QM and QM/MM) are also reported.