Revisiting the voronoi description of protein-protein interfaces: algorithms

• Authors: Frederic Cazals
• Venue: PRIB'10 Proceedings of the 5th IAPR international conference on Pattern recognition in bioinformatics
• Year: 2010

Describing macro-molecular interfaces is key to improve our understanding of the specificity and of the stability of macromolecular 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.