24 Problem of the Surface in Calculating Voronoi Volume

• If some of the neighbors around an atom are missing, the constructed polyhedron will be far too large to be physically "reasonable" and will allocate "too much" space to the atom. This is the problem with the protein surface, where one often does not have enough neighboring water atoms to construct reasonable polyhedra.
• Furthermore, when some neighbors are missing, even if an apparently reasonable polyhedron can be constructed, it will often have a very "pointy" or distended shape.
• Solution:
  • Create artificial shell of water positions around the protein.
  • Use molecular simulation to realistically position a waters around the protein.

Talk on Surfaces and Volumes / (C) Mark Gerstein (mbg@hyper.stanford.edu) / May 1996