A New Method for Mapping the Molecular Surface of a Protein Structure Using a Spherical Self-Organizing Map.

Abstract

A spherical self-organizing map (SSOM) was applied for mapping the molecular surface of a protein structure on a spherical structure. The active site of the X-ray crystal structure of β2 receptor protein was used for this purpose. After mapping the molecular surface points and assigning the associated molecular electrostatic potential (MEP) values, the original 3D structure of the active site was well reproduced by the SSOM. In order to validate the geometrical transformation and the resulting MEP distribution, the molecular surfaces of twenty β2 ligands were mapped on the established SSOM sphere. The MEP values of two spheres derived from the ligand and the β2 receptor protein were compared. In almost all cases of strong ligands, the two spheres had a moderate negative correlation.