Molecular surface design with balls

Nico Kruithof

In molecular modeling it is often necessary to define a molecular surface for further analysis and visualization of molecules. There are several classes of surfaces that are used to model the molecules, each with its own properties. We consider the molecular models that represent classical atoms as spheres whose radius, namely the van der Waals radius, indicates the largest distance at which an atom repels its neighbors. Models that fall in this category include the van der Waals surface, the Solvent Accessible Surface, the Solvent Excluded Surface or Connolly surface and the skin surface. The difference between the surfaces is the way the balls, the atoms, are glued together. The van der Waals surface and the Solvent Accessible Surface are defined as the boundary of the union of balls. The Solvent Excluded Surface is defined by spherical and toroidal patches that are formed by rolling a ball, representing the solvent, over the union of the balls. And the skin surface is defined by spherical and hyperbolic patches. Another class of surfaces, called Envelope surfaces, form a generalization of skin surfaces. Where the size of the patches is globally controlled for skin surface, envelope surfaces allow for local control over the size of the patches that form the glue between the different balls. In the presentation, each of these models is explained and different geometric properties of these surfaces are discussed. The main focus will be on skin surfaces and envelope surfaces.