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Assessing the Reconstruction of Macro-molecular Assemblies with Toleranced Models

Tom Dreyfus 1 Valérie Doye 2 Frédéric Cazals 1, * 
* Corresponding author
1 ABS - Algorithms, Biology, Structure
CRISAM - Inria Sophia Antipolis - Méditerranée
Abstract : We introduce Toleranced Models (TOM), a generic and versatile framework meant to handle models of macro-molecular assemblies featuring uncertainties on the shapes and the positions of proteins. A TOM being a continuum of nested shapes, the inner (resp. outer) ones representing high (low) confidence regions, we present statistics to assess features of this continuum at multiple scales. While selected statistics target topological aspects (pairwise contacts, complexes involving proteins of prescribed types), others are of geometric nature (geometric accuracy of complexes). We validate the TOM framework on recent average models of the Nuclear Pore Complex (NPC) obtained from reconstruction by data integration, and confront our statistics against experimental findings related to sub-complexes of the NPC. In a broader perspective, the TOM framework should prove instrumental to handle uncertainties of various kind, in particular in electron-microscopy and crystallography.
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Submitted on : Tuesday, October 25, 2011 - 3:52:25 PM
Last modification on : Saturday, June 25, 2022 - 11:06:51 PM
Long-term archiving on: : Thursday, November 15, 2012 - 10:31:06 AM


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  • HAL Id : inria-00635590, version 1


Tom Dreyfus, Valérie Doye, Frédéric Cazals. Assessing the Reconstruction of Macro-molecular Assemblies with Toleranced Models. [Research Report] RR-7768, INRIA. 2011. ⟨inria-00635590⟩



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