Rolling-sphere algorithm

The rolling sphere algorithm of Lee and Richards (1971) and a number of related algorithms yield the solvent accessible surface areas (Fig. 1). The radius of the solvent probe is near 1.5 A for water. The interface area B is the area of the protein surface that becomes buried at the interface when the two molecules associate, but, as the calculation uses only coordinates of the complex, it ignores conformation changes which may affect the accessible surface area of the components. The contribution of each molecule to B can be evaluated separately and is approximately equal to fr/2. Thus, other authors may prefer to quote values of fr/2 (Jones and Thornton, 1995, 1996). However, when the surfaces in contact have a strong curvature, the convex side tends to contribute more interface area than the concave side because accessible surface areas are measured one probe radius away from... 

Each lattice point or finite element in the system must be assigned to represent either part of the polyelectrolyte or its ionic environment. To account for a finite distance of closest approach to the polyelectrolyte surface by ions of varying size, a rolling-sphere algorithm may be... 

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