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Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins: A Practical Guide

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Book cover Structure and Function of Membrane Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2302))

Abstract

Current computer architectures, coupled with state-of-the-art molecular dynamics simulation software, facilitate the in-depth study of large biomolecular systems at high levels of detail. However, biological phenomena take place at various time and length scales and as a result a multiscale approach must be adopted. One such approach is coarse-graining, where biochemical accuracy is sacrificed for computational efficiency. Here, we present a practical guide to setting up and carrying out coarse-grained molecular dynamics simulations.

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Acknowledgments

The authors thanks Matthieu Chavent for details of UnityMol.

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Authors and Affiliations

  1. Department of Biochemistry, University of Oxford, Oxford, UK

    William G. Glass & Philip C. Biggin

  2. School of Chemistry, University of Southampton, Southampton, UK

    Jonathan W. Essex, Marley L. Samways & Syma Khalid

  3. Randall Centre for Cell & Molecular Biophysics, Kings College London, London, UK

    Franca Fraternali & Irene Marzuoli

  4. Scientific Computing Department, STFC Daresbury Laboratory, Warrington, UK

    James Gebbie-Rayet

Authors
  1. William G. Glass
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  2. Jonathan W. Essex
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  3. Franca Fraternali
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  4. James Gebbie-Rayet
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  5. Irene Marzuoli
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  6. Marley L. Samways
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  7. Philip C. Biggin
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  8. Syma Khalid
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Corresponding authors

Correspondence to Philip C. Biggin or Syma Khalid .

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Editors and Affiliations

  1. School of Biological Sciences and School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA

    Ingeborg Schmidt-Krey

  2. School of Physics, Georgia Institute of Technology, Atlanta, GA, USA

    James C. Gumbart

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Glass, W.G. et al. (2021). Coarse-Grained Molecular Dynamics Simulations of Membrane Proteins: A Practical Guide. In: Schmidt-Krey, I., Gumbart, J.C. (eds) Structure and Function of Membrane Proteins. Methods in Molecular Biology, vol 2302. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1394-8_14

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  • DOI: https://doi.org/10.1007/978-1-0716-1394-8_14

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1393-1

  • Online ISBN: 978-1-0716-1394-8

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