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    Protein structure fitting and refinement guided by cryo-EM density

    Topf, Maya and Lasker, K. and Webb, B. and Wolfson, H.J. and Chiu, W. and Sali, A. (2008) Protein structure fitting and refinement guided by cryo-EM density. Structure 16 (2), pp. 295-307. ISSN 0969-2126.

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    Abstract

    For many macromolecular assemblies, both a cryo-electron microscopy map and atomic structures of its component proteins are available. Here we describe a method for fitting and refining a component structure within its map at intermediate resolution (<15 Å). The atomic positions are optimized with respect to a scoring function that includes the crosscorrelation coefficient between the structure and the map as well as stereochemical and nonbonded interaction terms. A heuristic optimization that relies on a Monte Carlo search, a conjugate-gradients minimization, and simulated annealing molecular dynamics is applied to a series of subdivisions of the structure into progressively smaller rigid bodies. The method was tested on 15 proteins of known structure with 13 simulated maps and 3 experimentally determined maps. At

    Metadata

    Item Type: Article
    Keyword(s) / Subject(s): Proteins
    School: Birkbeck Schools and Departments > School of Science > Biological Sciences
    Research Centre: Bioinformatics, Bloomsbury Centre for, Structural Molecular Biology, Institute of (ISMB)
    Depositing User: Administrator
    Date Deposited: 04 Aug 2010 14:09
    Last Modified: 07 Dec 2016 15:02
    URI: http://eprints.bbk.ac.uk/id/eprint/1145

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