Molecular Dynamics Simulations of Protein–Drug Complexes: A Computational Protocol for Investigating the Interactions of Small-Molecule Therapeutics with Biological Targets and Biosensors

MD simulations provide a powerful tool for the investigation of protein-drug complexes. The following chapter uses the aryl acylamidase-acetaminophen system as an example to describe a general protocol for preparing and running simulations of protein-drug complexes, complete with a step-by-step tutorial. The described approach is broadly applicable toward the study of drug interactions in the context of both biological targets and biosensing enzymes.