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Revisiting the description of Protein-Protein interfaces. Part I: Algorithms

Frédéric Cazals 1 Flavien Proust
1 GEOMETRICA - Geometric computing
CRISAM - Inria Sophia Antipolis - Méditerranée
Abstract : The description of non-covalent contacts in (macro-)molecular assemblies is of fundamental interest for understanding the formation and the stability of such complexes. Unfortunately, the description of such contacts is usually carried out using pairwise distances and the Solvent Accessible Surface Area Lost upon formation of the complex - SASAL for short, but without distinguishing finer topological and geometric properties of the interface. The goal of this paper is to develop a notion of interface amenable to a finer topological and geometric analysis, providing more accurate physical and chemical information. Consider a complex made of two proteins $A$, $B$, and call $W$ the (crystallographic) water molecules. First, we define from the Voronoi diagram of the atomic balls an interface between $A$ and $B$, which is coherent with the atoms loosing accessibility to the solvent upon formation of the complex $A \cup B$, and accommodates the crystallographic water molecules. Second, we show how to study the topology (connected components and boundaries) and the geometry of interfaces. Third, we show how to weight the interface facets so as to recover the SASA lost upon formation of the complex, and extend the weighting scheme to accommodate atoms near the interface. Our interfaces are implemented using the CGAL library, and the corresponding module integrated to a VMD plug-in. A detailed experimental study on the usual protein-protein databases is provided in a companion paper.
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https://hal.inria.fr/inria-00070656
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Submitted on : Friday, May 19, 2006 - 9:08:05 PM
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Frédéric Cazals, Flavien Proust. Revisiting the description of Protein-Protein interfaces. Part I: Algorithms. RR-5346, INRIA. 2004, pp.28. ⟨inria-00070656⟩

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