Title: Visible Volume: A Robust Measure for Protein Structure Characterization.
Author: Loredana Lo Conte and Temple F. Smith
Date: March 20, 1997
Abstract:

We propose a new characterization of protein structure based on the natural
tetrahedral geometry of the beta carbon and a new geometric measure of
structural similarity, called visible volume. In our model, the
side-chains are replaced by an ideal tetrahedron, the orientation of which is
fixed with respect to the backbone and corresponds to the preferred rotamer
directions. Visible volume is a measure of the non-occluded empty space
surrounding each residue position after the side-chains have been removed. It
is a robust, parameter-free, locally-computed quantity that accounts for all
spatial constraints that are of relevance to the corresponding position in
the native structure. When computing visible volume, we ignore the nature of
both the residue observed at each site and the ones surrounding it. We focus
instead on the space that, together, these residues could occupy.  By doing
so, we are able to quantify a new kind of invariance beyond the apparent
variations in a protein family, namely, the conservation of the physical
space that is available at structurally equivalent positions for 3-D
side-chain packing. Visible volume has the unique property of estimating how
much space can be used at each site for different combinations of side-chains
to fit in. This property, and the relation of visible volume to the degree of
exposure of a residue position, qualify it as a powerful tool in a variety of
applications, from the detailed analysis of protein structure to the
definition of better scoring functions for threading purpose.