Probing a Continuum of Macro-molecular Assembly Models with Graph Templates of Complexes

Tom Dreyfus 1 Valérie Doye 2 Frédéric Cazals 1, *
* Corresponding author
1 ABS - Algorithms, Biology, Structure
CRISAM - Inria Sophia Antipolis - Méditerranée
Abstract : Reconstruction by data integration is an emerging trend to reconstruct large protein assemblies, but uncertainties on the input data yield average models whose quantitative interpretation is challenging. This paper presents methods to probe fuzzy models of large assemblies against atomic resolution models of sub-systems. More precisely, consider a Toleranced Model (TOM) of a macro-molecular assembly, namely a continuum of nested shapes representing the assembly at multiple scales. Also consider a template namely an atomic resolution 3D model of a sub-system (a complex) of this assembly. We present graph-based algorithms performing a multi-scale assessment of the complexes of the TOM, by comparing the pairwise contacts which appear in the TOM against those of the template. We apply this machinery to recent average models of the Nuclear Pore Complex, and confront our observations to the latest experimental work.
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Tom Dreyfus, Valérie Doye, Frédéric Cazals. Probing a Continuum of Macro-molecular Assembly Models with Graph Templates of Complexes. [Research Report] RR-8118, INRIA. 2012, pp.20. ⟨hal-00745558v2⟩

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