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... 

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... 

Connolly J. A. D. and Kerrick D. M. (1987). An algorithm and computer program for calculating composition phase diagrams. CALPHAD, 11 1-55. 

The strategy used in this review to dissect specific fundamental interactions is to isolate first the hydrophobic effects and subsequently other interactions. Within this context the hydrophobic effect is defined as that contribution to the overall thermodynamics of a process that is proportional to the amount of apolar surface that becomes exposed to the solvent (Hermann, 1972 Gill and Wadso, 1976 Livingstone etal, 1991). The apolar surface area exposed to solvent can be computed using various algorithms (Lee and Richards, 1971 Hermann, 1972 Shrake and Rupley, 1973 Connolly, 1983) that yield the accessible surface area (ASA) in units of square angstroms (A2). 

Unlike many other continuum approaches, PCM adopts cavities of realistic shape modelled on the solute atoms they are built according to GePol algorithm, [114] in which the cavity is defined as the envelope of spheres centred on solute atoms or atomic groups. Besides the atomic spheres, other spheres are added by GePol to smooth the solute-solvent boundary, approximating the so-called solvent accessible surface proposed by Connolly. 

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. 

Other ASC solvation methods use Connolly s algorithm (Connolly, 1983 1985) to define Sse and to provide a tessellation of the surface. GEPOL gives surface and volume, values which are more accurate and at a lower cost than Connolly s algorithm (Pascual-Ahuir and Silla 1990 Pascual-Ahuir et... 

To evaluate f f the van der Waals spheres are not sufficient. The analytical definition of f0bs is often replaced by approximate expressions, a set of additional spheres as in GEPOL (Pascual-Ahuir et al. 1987), by analytical functions as in Connolly s algorithm (Connolly, 1983) and in DefPol (Pomelli and Tomasi, 1995). 

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. 

Connolly developed a computational technique for docking two protein structures based on matching complementary patterns of knobs and holes (106). The algorithm was used to predict the association of the a and fi subunits of hemoglobin to form the corrext a-/ dimer. 

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. 

M. L. Connolly. Depth buffer algorithms for molecular modeling./ Mol. Graph., 3 19-24,1985. 

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