Abstract

Common geometric models for proteins and other molecules are the space filling diagram, the solvent ac-cessible surface, and the molecular surface. We descnbe software that compules metric properties of these mod-els, including volume and surface area. It also mea-sures voids or empty space enclosed by the protein, and it keeps track of surface area contributions of individ-ual atoms. The software is based on J-dimensional alpha complexes and on inclusion-exclusion formulas with terms derived from the simplices in this com-plex. The so,ftware is available via anonymous ftp at ftp.ncsa.uiuc.edu. 1 Introduct ion The space filling dzagram, SF, introduced by Lee and Richards [ll], models a protein as the union of possibly overlapping spherical balls in R3, see figure 1. Each ball represents an atom and its size is determined by the van der Waals radius of the atom. A void is a piece *This work is supported by the National Science Founda-tion, under grant ASC-9200301, the CISE postdoctoral fellow-

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