Accessible surface area

The accessible surface area (ASA) or solvent accessible surface area (SASA) is the surface area of a biomolecule that is accessible to a solvent. Measurement of ASA is usually described in units of square angstroms (a standard unit of measurement in molecular biology). ASA was first described by Lee & Richards in 1971 and is sometimes called the Lee Richards molecular surface. ASA is typically calculated using the 'rolling ball' algorithm developed by Shrake & Rupley in 1973. This algorithm uses a sphere (of solvent) of a particular radius to 'probe' the surface of the molecule.

The Shrake–Rupley algorithm is a numerical method that draws a mesh of points equidistant from each atom of the molecule and uses the number of these points that are solvent accessible to determine the surface area. The approximations used in LCPO result in an error in the range of 1 3 Ų.

Recently, a method was presented that calculates ASA fast and analytically using a power diagram.

Accessible surface area is often used when calculating the transfer free energy required to move a biomolecule from an aqueous solvent to a non polar solvent, such as a lipid environment. The LCPO method is also used when calculating implicit solvent effects in the molecular dynamics software package AMBER. It is recently suggested that (predicted) accessible surface area can be used to improve prediction of protein secondary structure.

The ASA is closely related to the concept of the solvent excluded surface (also known as the Connolly's molecular surface area or simply Connolly surface), which is imagined as a cavity in bulk solvent. It is also calculated in practice via a rolling ball algorithm developed by Frederic Richards and implemented three dimensionally by Michael Connolly in 1983 and Tim Richmond in 1984. Connolly spent several more years perfecting the method.