MMBJC
Beckman 402
3:30 PM Wednesday 8 June 1994
        
                Coarse Representations
      for the Essential Features of the Protein Surface

                    Mark Gerstein

The protein surface is usually represented (and viewed) in terms of
thousands of intersecting atoms (spheres). The great amount of detail
in such a representation obscures the overall shape of the surface and
creates computational problems for many popular docking and surface
matching schemes. Two approaches are presented for removing
unnecessary detail and representing the essential features of the
protein surface.

(1) Reverse-crystallography: The protein surface is represented in
terms of a resolution-dependent Fourier series. This approach allows
for hierarchical, resolution-sensitive shape matching and very
efficient docking.

(2) The hydration surface: The protein surface is defined by the
second shell of water molecules surrounding it. The hydration surface
is similar to the commonly used molecular surface, but the "probe"
water positions are determined in the course of a molecular
simulation, rather than just purely geometrically, so it is argued
that this surface is more chemically meaningful.