Computation of the van der Waals volume and the molecular volume of a molecule based on the beta-complex

Abstract

A molecule consists of a set of atoms with van der Waals radii. The volume of the union of the atoms is called the van der Waals volume. A molecule is also associated with the molecular surface, or sometimes called the Connolly surface, which is de�ed by the blending of the molecule with a spherical probe. Then, the molecular volume is the volume contained within the molecular surface. It is well-known that these volumes are very important parameters in understanding the properties of the molecule and are hard to compute both correctly and e�iently. In this talk, we will present algorithms for these volumes (and the areas of the corresponding surfaces) correctly and e�iently based on the recent theory of beta- complex. Hosts:PMI, POSTECH BK21, POSTECH BSRI, NCRC for Systems Bio-Dynamics 8