Revisiting the Voronoi Description of Protein-Protein Interfaces: Algorithms

  • Frederic Cazals
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6282)

Abstract

Describing macro-molecular interfaces is key to improve our understanding of the specificity and of the stability of macro-molecular interactions, and also to predict complexes when little structural information is known. Ideally, an interface model should provide easy-to-compute geometric and topological parameters exhibiting a good correlation with important bio-physical quantities. It should also be parametric and amenable to comparisons. In this spirit, we recently developed an interface model based on Voronoi diagrams, which proved instrumental to refine state-of-the-art conclusions and provide new insights.

This paper formally presents this Voronoi interface model. First, we discuss its connexion to classical interface models based on distance cut-offs and solvent accessibility. Second, we develop the geometric and topological constructions underlying the Voronoi interface, and design efficient algorithms based on the Delaunay triangulation and the α-complex.

We conclude with perspectives. In particular, we expect the Voronoi interface model to be particularly well suited for the problem of comparing interfaces in the context of large-scale structural studies.

Keywords

Protein interfaces Computational Geometry Voronoi diagrams Geometric patterns 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Frederic Cazals
    • 1
  1. 1.INRIA Sopha-AntipolisFrance

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