ABSTRACT
The protein surface is defined as all the points of the van der Walls surface (vdWS) that are touched by a solvent sphere with a given radius. There are a few possibilities to define and represent the protein surface: vdWS, contact surface, molecular surface, and accessible solvent area also called the solvent accessible surface area. A precise representation of the protein surface is important for studying diverse biological processes at the molecular level, such as protein folding and stability, protein-ligand, and protein-protein interactions. It plays a central role in computational applications concerning protein crystal packing, enzyme catalysis, drug design, and molecular docking. The protein surface has not a uniformly distributed roughness, and therefore it has not a constant fractal dimension over all scales. The shape and chemical properties of the protein surface are essential for many phenomena such as: binding and diffusion of small molecules, absorption, heterogeneous catalysis, interactions with other proteins or nucleic acids and interactions with solid materials.
