It is widely believed that the geometry of a protein plays a crucial role in its folding process as well as in its interactions with other bio-molecules or small ligands, yet geometrical methods are still uncommon in computational biology because several unresolved representational and algorithmic issues remain. ProShape is designed to provide answers to some of these issues.

ProShape is an ongoing effort, whose aim is to develop new computational techniques for simulating, analyzing and visualizing protein structures. It will provide access to new software whose aim is to help structural biologists with their research.

Surface, Volume and Protein Energetics
The accurate modeling of protein in solution using molecular mechanics requires realistic models for the interaction of the solvent with the molecule. To treat such a medium (usually water) in a molecular calculation, both explicit and implicit solvent models have been developed. While explicit models rely on using hundreds or thousands of discrete solvent molecules, implicit solvent models treat the solvent as a continuous medium having the average properties of the real solvent, and surrounding the solute beginning at the van der Waals surface. Most continuum models relate the energetics of the interaction of the solvent with the protein to the geometry of this surface. A small review of implicit solvent models is available here.