Three different decoy sets were aligned and scored against an SE derived from the respective crystal structure. The first was monoclonal antibody Fab fragment (PDB code 1baf, 60 models), the second was Yellow Tuna myoglobin protein (PDB code 1myt, 58 models), and the third was monoclonal antibody Fab fragment (PDB code 1dvf, 61 models). Note the points at the top of the graph for 1dvf (which result from principal component alignment [PCA]) are discussed in Results. They result from an improper model orientation when PCA is used.