An effective method of electrostatic potential calculation on protein binding site

During protein molecules binding process, electrostatic interaction plays a crucial role. Calculation of electrostatic potential on protein binding site is important for studying protein structure and function. We design an algorithm to calculate electrostatic potentials between the aromatic rings in the bound ligands and nucleic acids and their cognate proteins. By analyzing a diverse set of complex structures, we have found that the electrostatic potentials of the carbon atoms of an aromatic ring are higher than those of methyl/methylene atoms in the same molecule. The discovery can greatly improve molecular docking efficiency and accuracy.