ISSN:
1434-6036
Keywords:
PACS. 87.10.+e General theory and mathematical aspects – 36.20.-r Macromolecules and polymer molecules
Source:
Springer Online Journal Archives 1860-2000
Topics:
Physics
Notes:
Abstract: 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.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1140/epjb/e2003-00176-5
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