Identification of substrate channels and protein cavities

A grid-based algorithm is presented for identifying and displaying channels and cavities in a given protein structure. A point on a regular Cartesian grid is defined to be located in a cavity or a channel if the point has neighbouring grid points in the direction of at least two Cartesian axes, which are located inside the molecule. The cavities or channels can be displayed as clusters of these grid points or as the part of the surface and the amino acid residues lying next to these grid points. The algorithm was tested successfully using the gramicidin A dimer, different cytochrome P450's, and the proteolytic enzyme trypsin.