ALGORITHMS FOR EVALUATING THE LONG-RANGE ACCESSIBILITY OF PROTEIN SURFACES

Algorithms are presented for characterizing the long-range accessibili ties of protein surfaces. First, we describe an analytical method for determining the maximum contact radius for each atom in a structure. T he problem is simplified greatly by geometric inversion in a sphere, a type of conformal mapping. Second, we introduce the concept of diffus ion accessibility of a protein surface, which we evaluate either by ra ndom-walk simulations or by numerical solution of the equations of dif fusion with the protein acting as an adsorber. These two measures of e xposure are compared to each other as well as to the more common notio n of solvent accessibility. These new procedures provide longer-range descriptions of surface geometry which may be useful in docking studie s and other areas where surface comparison is required.