Solvent-accessible surface, overlapping

Fig. 8.1 The surface area of a molecule from overlapping spheres and from the surface generated by a sphere rolling over the molecular surface. Like the solvent, the rolling sphere cannot reach into V-shaped cavities, so the area of the surface it defines is a more realistic measure of the solvent-accessible surface than is the overlapping-spheres surface...

T. J. Richmond, /. Mol. Biol., 178, 63 (1984). Solvent Accessible Surface Area and Excluded Volume in Proteins—Analytical Equations for Overlapping Spheres and Implications for the... 

A further class of ligand-based 3D-methods focuses on the comparison of the shape of molecules. This is done either on the basis of a solvent accessible surface or the shape is approximated by atom-centered soft Gaussian functions. Maximizing the overlay of these Gaussian functions maximizes the overlap between a query molecule and a single conformation of the target molecule. This is used in the Rapid... 

When using the smoothed Coulomb potential description, one first wished to emphasize the overlap of the electrostatic potential acting in regions of space remote from the molecular skeleton itself, that is, beyond the so-called solvent accessible surface of the molecule. In that case, one first used the overlap similarity measure with the Hodgkin similarity index as Good et al. [44] reported that this last index is sensitive to the magnimde of the 3D descriptor field. It, however, appeared that the Laplacian-Tanimoto combination was more efficient. 

The coefficients D0 and Di are determined from experimental solvation free energies of linear hydrocarbons. The solvent accessible area is the area formed from overlapping spheres centered at the atom positions with radii equal to vdW radii increased by a probe radius. This surface area definition is usually used in Eq. (35). Depending on the set of vdW radii used and the probe radii (usually 1.4 A), the coefficients D0 and Di are approximately equal to 0.85 kcal/mol and 0.005 kcal/mol/A2, respectively. 

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