Solvent-accessible Surfaces of Proteins and Nucleic Acids

In this chapter we discuss many applications of the dot surface numerical algorithm. It has been necessary to invent an analytical surface algorithm to generate high-resolution color raster display images and to compute more accurate molecular areas and volumes. A solvent-accessible area was originally defined and computed as the area traced out by the center of a probe sphere representing a solvent molecule as it is rolled over the surface of the molecule of interest. These computational methods were invented as tools that could be used to attack the protein-folding problem. The problem is predicting the three-dimensional structure of a protein given only its primary sequence of amino acids. Simply measuring the size of an area is insufficient for the study of many aspects of protein and nucleic acid function such as substrate binding and catalysis, drug-nucleic acid interaction, and recognition by the immune system. This method has proved useful in enzymology, immunology, virology, molecular pathology, and the study of protein-ligand and protein-protein interactions.