Skip to Main content Skip to Navigation
Conference papers

Revisiting the Voronoi Description of Protein-Protein Interfaces: Algorithms

Frédéric Cazals 1, *
* Corresponding author
1 ABS - Algorithms, Biology, Structure
CRISAM - Inria Sophia Antipolis - Méditerranée
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.

Complete list of metadatas

Cited literature [8 references]  Display  Hide  Download

https://hal.inria.fr/hal-00796062
Contributor : Service Ist Inria Sophia Antipolis-Méditerranée / I3s <>
Submitted on : Friday, March 1, 2013 - 3:29:31 PM
Last modification on : Thursday, March 5, 2020 - 5:34:20 PM
Document(s) archivé(s) le : Sunday, June 2, 2013 - 4:01:31 AM

File

voronoi-interfaces-algorithm_p...
Files produced by the author(s)

Identifiers

Collections

Citation

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⟩

Share

Metrics

Record views

348

Files downloads

375