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Geometric, topological and contact analysis of interfaces in macro-molecular complexes: from the atomic to the complex scale using Intervor

Frédéric Cazals 1
1 GEOMETRICA - Geometric computing
CRISAM - Inria Sophia Antipolis - Méditerranée
Abstract : Understanding the sociology of interactions between the proteins encoded in a genome is a central question of structural biology, and interface models between molecules forming a complex are instrumental in this perspective. Qualifying interface atoms as atoms loosing solvent accessibility in the complex, or pairs of atoms within a distance threshold, several interface models have been proposed. Yet, until recently, no interface model existed to answer coherently (if at all) the following questions: can one bridge the gap from atoms loosing solvent accessibility to interface pairs? is the interface flat or curvy? is it connected or not (does it have a multi-patch structure)? is a connected component of the interface simply connected or not (does it have a hole)? what is precisely the role played by interface structural water? Using the $\alpha$-complex of the Van der Waals balls, a construction derived from the Voronoi diagram, we designed such an interface model, and validated it on the usual database of co-crystallized protein-protein complexes. This paper is a methodological paper aiming at easing the access of the interface model to structural biologists. As such, the paper overviews: (i) the geometric principles underlying the interface model (ii) the definitions of the interface and its extension to accommodate structural water (iii) the statistics one can compute from the interface model (iv) the Software Intervor and the associated web site. These presentations are accompanied by illustrations and insights on protein - protein complexes.
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https://hal.inria.fr/inria-00070162
Contributor : Rapport de Recherche Inria <>
Submitted on : Friday, May 19, 2006 - 7:17:51 PM
Last modification on : Saturday, January 27, 2018 - 1:31:28 AM
Long-term archiving on: : Tuesday, February 22, 2011 - 11:37:33 AM

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  • HAL Id : inria-00070162, version 1

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Frédéric Cazals. Geometric, topological and contact analysis of interfaces in macro-molecular complexes: from the atomic to the complex scale using Intervor. [Research Report] RR-5864, INRIA. 2006, pp.36. ⟨inria-00070162⟩

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