The Laguerre polyhedral decomposition: application to protein folds

An extension of the Voronoi tessellation, the Laguerre polyhedral decomposition, is introduced and applied to the analysis of the packing geometry of amino-acids in folded proteins. This method considers an ensemble of points with different weights and therefore it is well suited for a geometrical analysis of a set of objects with a wide size distribution. With this method it is shown that the true volumes occupied by the amino-acids inside a protein is better described than with the standard Voronoi procedure. This method allows defining unambiguously (without cut-off distance) the neighborhood for each amino-acid in a given protein and contact matrices can be established which contain all topological informations on the internal structure. Finally, a, statistical analysis of the geometrical characteristics of the polyhedra attached to each amino-acid is done over a collection of 35 proteins.