Volarea - a bioinformatics tool to calculate the surface area and the volume of molecular systems.

We have developed a computer program named 'VolArea' that allows for a rapid and fully automated analysis of molecular structures. The software calculates the surface area and the volume of molecular structures, as well as the volume of molecular cavities. The surface area facility can be used to calculate the solvent-exposed surface area of a molecule or the contact area between two molecules.

Metals in proteins: cluster analysis studies.

We have conducted a prospective analysis of the Protein Data Bank in order to study certain constituents of proteins: elements that are neither halogens nor phosphorus nor part of the biological amino acid set. A sample of 5749 structures was analyzed and classified according to the 56 elements encountered. Fifteen metals (Na, Mg, K, Ca, Mn, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, W, Hg) are involved in almost half of the structures, with each metal figuring in more than 100 structures.