Molecular surface Connolly algorithm

Molecular surfaces defined on the basis of the Connolly algorithm (see Section II) can be effectively used in the interactive treatment of molecular scenarios. These surfaces are a representation of the repulsive... 

The area of the solvent-accessible surface is called the Solvent-Accessible Surface Area SASA (or Total Solvent-Accessible Surface Area, TSASA). Several algorithms were proposed that implement both the first original definition of SASA and that of Richards. One of the most popular algorithms that implements Richards solvent-accessible surface was proposed by Connolly [Connolly, 1983a]. It is an analytical method for computing molecular surface, and is based on surface decomposition into a set of curved regions of spheres and tori that join at circular arcs spheres, tori and arcs are defined by analytical expressions in terms of atomic coordinates, van der Waals radii and the probe radius. Ihe molecular surface calculated in such a way is sometimes referred to as Connolly surface area. This algorithm also allows the calculation of solvent-accessible atomic areas. 

Connolly (43,44) and Richmond (45) also developed analytical methods for calculating molecular surface area and volume, which provide nearly exact values for the surface area and enclosed volume. Richmond s method provides analytical derivatives for surface area with respect to the cartesian coordinates of the atoms, which may be useful for docking (Section V). Connolly s algorithm also produces spectacular shaded raster graphics images (46), which give a very different feel for a macromolecular surface than conventional space-filling displays. 

Widely used algorithms for calculating the molecular and accessible surfaces were developed by Connolly [Connolly 1983a, b], and others [e.g. Richmond 1984] have described formulae for the calculation of exact or approximate values of the surface area. There are many ways to represent surfaces, some of which are illustrated in Figure 1.7 (colour plate section). As shown, it may also be possible to endow a surface with a translucent quality, which enables the molecule inside the surface to be displayed. Clipping can also be used... 

The surface area of the molecular envelope, A, is another important descriptor that also correlates with solvation properties. 442 Jhe computation of surface area is less accurate than the computation of volume. Most methods resort to a surface discretized as a distribution of points (the so-called Connolly surfacei ). Examples of methodologies and algorithms for evaluating surface areas are found elsewhere. 

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