In order to have protein files useable by FITTED, we developed the ProCESS module which assigns the advanced residue names, advanced hydrogen names, atom types, and charges for the protein. ProCESS creates the overlapping spheres by first generating an evenly spaced grid and keeping the points that do not clash with the protein.
Next the points are converted into spheres. For this purpose, each sphere is inflated until making contact with a protein atom center (slightly overlapping with the protein surface) or one of the grid edges. The obtained sphere size and center are archived. Smaller spheres, included in larger ones, are next removed in order to reduce the total number of spheres while still covering the entire cavity space. This step is carried out repeatedly until all spheres are examined. This step significantly reduces the number of spheres while approximating the whole cavity space.
The interaction sites are automatically created by ProCESS after the generation of the active site cavity. The hydrogen bond donor (HBD), acceptor (HBA) and hydrophobic (HYD) interaction sites are created by locating spheres complementary to the properties of the binding site residues.
