Solvent-Accessible Surfaces of Proteins and Nucleic Acids

TLDR

Previous molecular graphics used wire or space‑filling models, whereas this method displays only solvent‑accessible atoms and builds on the dot‑surface algorithm applied in enzymology, drug design, immunology, and DNA recognition. The study introduces a method for analytically computing a smooth, three‑dimensional contour around a molecule. The analytic surface can be rendered on raster or vector displays and permits calculation of molecular areas and volumes directly from the contour.

Abstract

A method is presented for analytically calculating a smooth, three-dimensional contour about a molecule. The molecular surface envelope may be drawn on either color raster computer displays or real-time vector computer graphics systems. Molecular areas and volumes may be computed analytically from this surface representation. Unlike most previous computer graphics representations of molecules, which imitate wire models or space-filling plastic spheres, this surface shows only the atoms that are accessible to solvent. This analytical method extends the earlier dot surface numerical algorithm, which has been applied in enzymology, rational drug design, immunology, and understanding DNA base sequence recognition.