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Protein–ligand binding occurs through interactions at the molecular surface. Hence, a proper description of this surface is essential to our understanding of the process of molecular recognition. Recent studies have noted the inadequacy of using a fixed 1.4 Å solvent probe radius to generate the molecular surface. This assumes that water molecules approach all surface atoms at an equal distance irrespective of polarity, which is not the case. To adequately model the protein–water boundary requires that the solvent probe radius change according to the polarity of its contacting atoms, smaller near polar atoms and larger near apolar atoms. To our knowledge, no method currently exists to generate the molecular surface of a protein in this manner. Using a modification of the marching tetrahedra algorithm, we present a method to generate molecular surfaces using a variable radius solvent probe. The resulting …