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Biomolecular structure refinement using the GROMOS simulation software

Schmid, Nathan ; Allison, Jane ; Dolenc, Jožica ; Eichenberger, Andreas ; Kunz, Anna-Pitschna ; van Gunsteren, Wilfred

In: Journal of Biomolecular NMR, 2011, vol. 51, no. 3, p. 265-281

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    Titre
    • Biomolecular structure refinement using the GROMOS simulation software
    Auteur
    • Schmid, Nathan. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093, Zürich, Switzerland
    • Allison, Jane. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093, Zürich, Switzerland
    • Dolenc, Jožica. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093, Zürich, Switzerland
    • Eichenberger, Andreas. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093, Zürich, Switzerland
    • Kunz, Anna-Pitschna. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093, Zürich, Switzerland
    • van Gunsteren, Wilfred. Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093, Zürich, Switzerland
    Type de document
    • Postprint
    Langue
    • Inglese
    Publié dans
    • Journal of Biomolecular NMR, 2011, vol. 51, no. 3, p. 265-281. Springer Netherlands
    Autre version électronique
    Identifiant OAI-PMH
    • oai:doc.rero.ch:313099
    Summary
    For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, 3 J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation