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Cryo-Electron Microscopy Modeling by the Molecular Dynamics Flexible Fitting Method

Authors

  • Kwok-Yan Chan,

    1. Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
    2. Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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  • Leonardo G. Trabuco,

    1. CellNetworks, University of Heidelberg, 69120 Heidelberg, Germany
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  • Eduard Schreiner,

    1. Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
    Current affiliation:
    1. BASF SE, 67063 Ludwigshafen, Germany
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  • Klaus Schulten

    Corresponding author
    1. Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801
    2. Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
    • Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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  • This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Abstract

The increasing power and popularity of cryo-electron microscopy (cryo-EM) in structural biology brought about the development of so-called hybrid methods, which permit the interpretation of cryo-EM density maps beyond their nominal resolution in terms of atomic models. The Cryo-EM Modeling Challenge 2010 is the first community effort to bring together developers of hybrid methods as well as cryo-EM experimentalists. Participating in the challenge, the molecular dynamics flexible fitting (MDFF) method was applied to a number of cryo-EM density maps. The results are described here with special emphasis on the use of symmetry-based restraints to improve the quality of atomic models derived from density maps of symmetric complexes; on a comparison of the stereochemical quality of atomic models resulting from different hybrid methods; and on application of MDFF to electron crystallography data. © 2012 Wiley Periodicals, Inc. Biopolymers 97: 678–686, 2012.

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