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Revisiting the Voronoi description of protein–protein interfaces
Author(s) -
Cazals Frédéric,
Proust Flavien,
Bahadur Ranjit P.,
Janin Joël
Publication year - 2006
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.062245906
Subject(s) - voronoi diagram , curvature , interface (matter) , protein data bank , computer science , set (abstract data type) , biological system , statistical physics , protein structure , data mining , theoretical computer science , physics , mathematics , molecule , geometry , biology , quantum mechanics , gibbs isotherm , nuclear magnetic resonance , programming language
We developed a model of macromolecular interfaces based on the Voronoi diagram and the related alpha‐complex, and we tested its properties on a set of 96 protein–protein complexes taken from the Protein Data Bank. The Voronoi model provides a natural definition of the interfaces, and it yields values of the number of interface atoms and of the interface area that have excellent correlation coefficients with those of the classical model based on solvent accessibility. Nevertheless, some atoms that do not lose solvent accessibility are part of the interface defined by the Voronoi model. The Voronoi model provides robust definitions of the curvature and of the connectivity of the interfaces, and leads to estimates of these features that generally agree with other approaches. Our implementation of the model allows an analysis of protein–water contacts that highlights the role of structural water molecules at protein–protein interfaces.