Application of Dynamics Perturbation Analysis (DPA) to predict protein functional sites. Left. In this example, the surface of lysozyme (PDB entry 1JEF , yellow cartoon) is decorated with test points (533 spheres at a density of 1 point per Å2), and the degree to which the test points individually perturb the protein conformational distribution is calculated (temperature-coded coloring of the spheres). A tri-NAG molecule (purple wireframe) binds in the active site. Warm-colored spheres indicate where the perturbation is large. Center. Points where the perturbation is largest are selected and clustered (green spheres). Right. Cα atoms within 6 Å of the DPA cluster are selected, and the associated residues define the predicted functional site (16 residues). For comparison, Cα atoms within 6 Å of the tri-NAG are selected; we use the associated residues to define the actual functional site (7 residues). The overlapping residues (6 residues) are shown in orange; there are 10 predicted residues that do not exactly match the functional site (green), and there is 1 functional site residue that is not among the predicted residues (purple, in the helix on the right hand side).