Multi-threading protein surface functional description

The paper presents an image-oriented description of artificial and biological nanostructured surfaces, with applicability to the functional characterization of atom neighborhoods at the surface of proteins. The property which is considered is the hydrophobicity around each surface atom. The actual hydrophobicity distribution on the atoms that form an atom´s vicinity is replaced by an equivalent hydrophobicity density distribution, computed in a standardized hexagonal or octagonal pattern around the atom. The software implementation is a desktop multi-threading application, able to process a large number of atom properties, such as type, 3D coordinates, charge and hydrophobicity. The atoms at the surface of a molecule are divided among the execution threads and a feature vector is created for each of them. The purpose of this work is to create a database of molecular surfaces that will be used in several nanotechnology research fields.