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Modeling Macro-Molecular Interfaces with Intervor

Frédéric Cazals 1, * Sebastien Loriot 1
* Corresponding author
1 ABS - Algorithms, Biology, Structure
CRISAM - Inria Sophia Antipolis - Méditerranée
Abstract : Intervor is a software computing a parameter free representation of macro-molecular interfaces, based on the alpha-complex of the atoms. Given two interacting partners, possibly with water molecules squeezed in-between them, Intervor computes an interface model which has the following characteristics: (i) it identifies the atoms of the partners which are in direct contact and those whose interaction is water mediated, (ii) it defines a geometric complex separating the partners, the Voronoi interface, whose geometric and topological descriptions are straightforward (surface area, number of patches, curvature), (iii) it allows the definition of the depth of atoms at the interface, thus going beyond the traditional dissection of an interface into a core and a rim. These features can be used to investigate correlations between structural parameters and key properties such as the conservation of residues, their polarity, the water dynamics at the interface, mutagenesis data, etc. Intervor can be run from the web site http://cgal.inria.fr/abs/Intervor , or in stand-alone mode upon downloading the binary file. Plugins are also made available for Visual Molecular Dynamics (VMD) and Pymol.
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https://hal.inria.fr/inria-00426041
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Submitted on : Monday, October 26, 2009 - 10:40:42 AM
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Frédéric Cazals, Sebastien Loriot. Modeling Macro-Molecular Interfaces with Intervor. [Research Report] RR-7069, INRIA. 2009, pp.15. ⟨inria-00426041⟩

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