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

作者：Hasegawa Kiyoshi^*; Funatsu Kimito

来源：Molecular Informatics, 2012, 31(2): 161-166.

DOI：10.1002/minf.201100161

• ss 2 Receptor protein
• Chemogenomics
• Molecular electrostatic potential
• Molecular surface
• Spherical self-organizing map

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 beta 2 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 beta 2 ligands were mapped on the established SSOM sphere. The MEP values of two spheres derived from the ligand and the beta 2 receptor protein were compared. In almost all cases of strong ligands, the two spheres had a moderate negative correlation.

• 出版日期2012-2