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Protein Science (2006), 15:2082-2092. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society
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Revisiting the Voronoi description of protein–protein interfaces

Frédéric Cazals1, Flavien Proust1, Ranjit P. Bahadur2 and Joël Janin2

1 INRIA Sophia-Antipolis, Project Geometrica, F-06902 Sophia-Antipolis, France
2 IBBMC, UMR 8619, CNRS, Université Paris-Sud, F-91405 Orsay, France

(RECEIVED March 27, 2006; FINAL REVISION May 3, 2006; ACCEPTED May 3, 2006)

We developed a model of macromolecular interfaces based on the Voronoi diagram and the related alpha-complex, and we tested its properties on a set of 96 protein–protein complexes taken from the Protein Data Bank. The Voronoi model provides a natural definition of the interfaces, and it yields values of the number of interface atoms and of the interface area that have excellent correlation coefficients with those of the classical model based on solvent accessibility. Nevertheless, some atoms that do not lose solvent accessibility are part of the interface defined by the Voronoi model. The Voronoi model provides robust definitions of the curvature and of the connectivity of the interfaces, and leads to estimates of these features that generally agree with other approaches. Our implementation of the model allows an analysis of protein–water contacts that highlights the role of structural water molecules at protein–protein interfaces.

Keywords: protein–protein interaction; algorithmic geometry; alpha-complex; interface connectivity


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