Revisiting the Voronoi Description of Protein-Protein Interfaces: Algorithms

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


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.


Protein interfaces Computational Geometry Voronoi diagrams Geometric patterns 


  1. [BCR+04]
    Bahadur, R., Chakrabarti, P., Rodier, F., Janin, J.: A dissection of specific and non-specific protein–protein interfaces. JMB 336(4), 943–955 (2004)CrossRefGoogle Scholar
  2. [BER04]
    Ban, Y.-E.A., Edelsbrunner, H., Rudolph, J.: Interface surfaces for protein-protein complexes. In: RECOMB, San Diego, pp. 205–212 (2004)Google Scholar
  3. [BGNC09]
    Bouvier, B., Grünberg, R., Nilges, M., Cazals, F.: Shelling the voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics and composition. Proteins 76(3), 677–692 (2009)CrossRefPubMedGoogle Scholar
  4. [BT98]
    Bogan, A.A., Thorn, K.S.: Anatomy of hot spots in protein interfaces. J. Mol. Biol. 280 (1998)Google Scholar
  5. [CCJ99]
    Lo Conte, L., Chothia, C., Janin, J.: The atomic structure of protein-protein recognition sites. JMB 285(5), 2177–2198 (1999)CrossRefGoogle Scholar
  6. [CJ02]
    Chakrabarti, P., Janin, J.: Dissecting protein-protein recognition sites. Proteins 47(3), 334–343 (2002)CrossRefPubMedGoogle Scholar
  7. [CPBJ06]
    Cazals, F., Proust, F., Bahadur, R., Janin, J.: Revisiting the voronoi description of protein-protein interfaces. Protein Science 15(9), 2082–2092 (2006)CrossRefPubMedPubMedCentralGoogle Scholar
  8. [Ede92]
    Edelsbrunner, H.: Weighted alpha shapes. Technical Report UIUCDCS-R-92-1760, Dept. Comput. Sci., Univ. Illinois, Urbana, IL (1992)Google Scholar
  9. [GC05]
    Guharoy, M., Chakrabarti, P.: Conservation and relative importance of residues across protein-protein interfaces. PNAS 102(43), 15447–15452 (2005)CrossRefPubMedPubMedCentralGoogle Scholar
  10. [GLN04]
    Grünberg, R., Leckner, J., Nilges, M.: Complementarity of structure ensembles in protein-protein binding. Structure 12(12), 2125–2136 (2004)CrossRefPubMedGoogle Scholar
  11. [JT96]
    Jones, S., Thornton, J.M.: Principles of protein-protein interactions. PNAS 93(1), 13 (1996)CrossRefPubMedPubMedCentralGoogle Scholar
  12. [LC10]
    Loriot, S., Cazals, F.: Modeling macro-molecular interfaces with intervor. Bioinformatics 26(7), 964–965 (2010)CrossRefPubMedGoogle Scholar
  13. [MRL07]
    Mihalek, I., Reš, I., Lichtarge, O.: On itinerant water molecules and detectability of protein–protein interfaces through comparative analysis of homologues. JMB 369(2), 584–595 (2007)CrossRefGoogle Scholar
  14. [San79]
    Santaló, L.: Integral Probability and Geometric Probability. Encyclopedia of Mathematics and its Applications, vol. 1. Addison-Wesley, Reading (1979)Google Scholar
  15. [Tar83]
    Tarjan, R.E.: Data Structures and Network Algorithms. CBMS-NSF Regional Conference Series in Applied Mathematics, vol. 44. Society for Industrial and Applied Mathematics, Philadelphia (1983)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

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

Personalised recommendations