title: Probing a continuum of macro-molecular assembly models with graph templates of complexes.
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 article presents methods to probe fuzzy models of large assemblies against atomic resolution models of subsystems. Consider a toleranced model (TOM) of a macromolecular 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 subsystem (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 on TOM derived from an average model of the nuclear pore complex, to explore the connections among members of its well-characterized Y-complex.
authors.affiliation: INRIA Sophia-Antipolis-Méditerranée, Algorithms-Biology-Structure, 2004 route des Lucioles, BP 93, F-06902, Sophia-Antipolis, France.
authors.forename: Tom
authors.initials: T
authors.lastname: Dreyfus
authors.forename: Valérie
authors.initials: V
authors.lastname: Doye
authors.forename: Frédéric
authors.initials: F
authors.lastname: Cazals
mesh_terms: D000465:Algorithms; D046911:Macromolecular Substances; D008962:Models, Theoretical; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D046911:Macromolecular Substances; D011506:Proteins
keywords: isomorphic graphs; macro-molecular assemblies; maximum common subgraphs; model assessment; nuclear pore complex; reconstruction by data integration; toleranced models