The HARMONY programs can also compute the first and second derivatives of the surface parameterization. From these quantities, we can compute analytically the surface normal, surface area elements, and the principal curvatures.
An example of shape measures is shown here:
which shows the interface between the Cu-Zn superoxide dismutase dimer (SOD) in its crystallographic configuration.
This image shows surfaces of BPTI color-coded by the surface shape measure. This type of rendering improves the interpretation of the surfaces. This image was created using texture mapping instead of vertex colors so the rendering is very efficient.
In addition to computing a low-resolution representation of the surface geometry, HARMONY can also compute a low-resolution representation of surface properties. Important surface properties include hydrophobicity and electrostatic potential. The surface hydrophobicity of BPTI is represented here with the left surface computed by MSMS and the spherical harmonic surface on the right.
By computing low-resolution representations of these quantities, we can concentrate our docking efforts on putative complexes that are complementary at low-resolution and low-triangulation, and then check for complementarity at a higher resolution and higher triangulation.
We can also use the texture mapping technique to project surface properties from one surface to another. This image shows the binding site of Trypsin color-coded by the shape properties of BPTI.
Another important concern is the dynamics of protein structures. HARMONY can also represent the first-order surface motion computed by normal mode analysis. In these animations, the MSMS surface is on the right and the spherical harmonic representation of the surface geometry and the surface motion is on the left.
crambin normal modes 1 (500K mpeg)
crambin normal modes 2 (500K mpeg)