Molecular modeling techniques are widely used in medicinal chemistry for the study of biological targets, the rational design of new drugs, or the investigation of their mechanism of action. They are also applied in toxicology to identify chemical potential harmful effects. Molecular docking is a computational technique to predict the ligand binding mode and evaluate the interaction energy with a biological target. This chapter describes a computational workflow to predict possible endocrine disruptors on peroxisome proliferator-activated receptor alpha (PPARα), a nuclear receptor involved in glucose and lipid metabolism. The analyzed compounds are food contact chemicals, natural or synthetic substances intentionally added to food or released from the package or during production or technological processes.