Front matter

© 2004-2006 by Daniele Varrazzo

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Atom depth has been considered as a structural descriptor to correlate protein structure with folding and functional properties. The distance between an atom and the nearest water molecule or the closest surface dot has been proposed as a measure of the atom depth, but, in both cases, the three-dimensional character of depth is largely lost: an atom located at the bottom of a pocket may be at the same distance from the protein surface of an atom located in a protruding loop, but the former will be less accessible than the latter.

SADIC implements a new algorithm to calculate atom depth: it calculates the intersection between the molecular volume and spheres centered on the atoms whose depth has to be quantified. SADIC takes PDB files as input and can emit different measurements of exposed surfaces and volumes as well as a novel depth index, designed to promote comparison between atoms in a molecule and in different molecules.