Peroxisome proliferator activated receptor-alpha (PPAR-alpha) is a ligand-activated transcription factor which plays important roles in lipid and glucose metabolism. The aim of this work is to find residues which selectively recognize PPAR-alpha agonists and antagonists. To achieve this aim, PPAR-alpha/13M and PPAR-alpha/471 complexes were subjected to perform molecular dynamics simulations. This research suggests that several key residues only participate in agonist recognition, while some other key residues only contribute to antagonist recognition. It is hoped that such work is useful for medicinal chemists to design novel PPAR-alpha agonists and antagonists.