Revisiting the Voronoi Description of Protein-Protein Interfaces: Algorithms

Frédéric Cazals (1)

1 ABS - Algorithms, Biology, Structure

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.

Mots clés: Protein interfaces; Computational Geometry; Voronoi dia- grams; Geometric patterns

Domaines: Géométrie algorithmique [cs.CG]; Algorithme et structure de données [cs.DS]; Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]

Frédéric Cazals. Revisiting the Voronoi Description of Protein-Protein Interfaces: Algorithms. PRIB - 5th IAPR International Conference on Pattern Recognition in Bioinformatics - 2010, Sep 2010, Nijmegen, Netherlands. pp.419-430, ⟨10.1007/978-3-642-16001-1_36⟩. ⟨hal-00796062⟩