Fuzzy Molecular Surfaces

Abstract

Surface area of a macromolecule, accessible to a solvent, is defined and calculated, taking into account the probabilistic character of atomic positions due to the high frequency atomic vibrations. For a given a space point, we consider a probability of the event, that this point is covered by a macromolecule. A volume is defined as a space integral of this probability field. The envelope, accessible to a solvent molecule center, becomes fuzzy, existing only in a probabilistic sense. The accessible area is defined as a derivative of the envelope volume with respect to the probe size.

The accessible area thus defined has the advantage of being an analytic function of atomic coordinates and allows for an arbitrary (not necessarily spherical) probe geometry. Space integration is performed on a rectangular grid, using a third order Runge-Kutta integration scheme and the analytical subgrid averaging.