Abstract: In this paper we present a method for identifying and representing indentations, cavities and holes in a known protein structure. The identification procedure is performed initially. Once a pocket in the protein has been found, we use a boundary representation technique to represent it. Both the identification and the representation procedures rely upon modifications to the Marching Cubes algorithm of Lorensen and Cline [5], which can be used to give a piecewise planar representation of a three-dimensional object. The identification of a pocket essentially involves finding a point, (x0, y0, z0) say. The point should be such that a sphere of radius r can be centred there, without touching the centre of any atom in the protein, but there exists R > r such that a sphere of radius R centred at (x0, y0, z0) does touch the centre of an atom. If such a point is found, then it is deemed to be in a pocket. The boundary representation technique involves storing information about a boundary in the structure of a graph. The graph structure of a pocket, potential docking site, can then be compared to the graph structure of a candidate binding substrate using standard graph comparison algorithms. The required input for the algorithm is in the form of a Protein Data Bank (PDB) file.