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Local description of molecular surfaces

The paper presents a new approach for describing artificial and biological nanostructured surfaces. The atoms at the surface of a molecule are divided among the threads and a feature vector is created for each of them. The properties include the cumulated hydrophobicity in the neighborhood of each surface atom, represented in a standardized hexagonal pattern that approximates the actual surface distribution. The implementation is based on a Java Platform. The main benefits are the rich library, the powerful integration with other technologies and applications, as well as the large support community. The chosen architecture was a multi-threading one, able to process a large number of atom properties, such as type, 3D coordinates, charge and hydrophobicity, and to reduce the time request of the algorithm. In order to have a friendly and productive user interface, Java 2D and 3D packages have been used for canvases depicting atoms clusters at the molecule surface The purpose of this work is to create a database of molecular surfaces that will be used in several nanotechnology research fields.