https://doi.org/10.1140/epjb/e2003-00176-5
The Laguerre polyhedral decomposition: application to protein folds
1
Laboratoire de Physique des Solides, Université Paris Sud (associé au CNRS),
bâtiment 510, Centre d'Orsay, 91405 Orsay, France
2
Laboratoire des Verres, Université Montpellier 2 (associé au CNRS),
Place E. Bataillon Case 003, 34095 Montpellier, France
3
Laboratoire de Dynamique des Fluides Complexes, Université Louis Pasteur
(associé au CNRS), 3 rue de l'Université, 67084 Strasbourg, France
Corresponding author: a sadoc@lps.u-psud.fr
Received:
20
November
2002
Revised:
26
March
2003
Published online:
20
June
2003
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.
PACS: 87.10.+e – General theory and mathematical aspects / 36.20.-r – Macromolecules and polymer molecules
© EDP Sciences, Società Italiana di Fisica, Springer-Verlag, 2003