One important test to validate our docking workflow, confirm proper protein preparation, and evaluate the performance of the two scoring functions is self-docking. In this procedure, we re-dock the native ligand into its corresponding protein structure and compare the resulting geometry to the experimentally determined pose from the crystal structure. Achieving a relatively low RMSD between the re-docked and experimental geometries suggests that the protein preparation is at least reasonably accurate, with no major errors in the active site. It also indicates that the potential energy surface (PES) defined by the docking scoring function is reasonably aligned with the true PES.