Coarse-grained molecular dynamics simulations of membrane proteins: a practical guide
Coarse-grained molecular dynamics simulations of membrane proteins: a practical guide
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.
Membranes, Molecular dynamics, Molecular modelling, coarse-grained, membrane protein
253-273
Glass, William G.
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Essex, Jonathan W.
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Fraternali, Franca
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Marzuoli, Irene
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Samways, Marley Luke
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Biggin, Philip C.
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Khalid, Syma
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2021
Glass, William G.
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Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Fraternali, Franca
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Marzuoli, Irene
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Samways, Marley Luke
75cda5aa-31ef-4f62-9ea3-8655ea55d3fb
Biggin, Philip C.
c7394f79-450a-46c6-b77a-fadac30ded33
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Glass, William G., Essex, Jonathan W., Fraternali, Franca, Marzuoli, Irene, Samways, Marley Luke, Biggin, Philip C. and Khalid, Syma
(2021)
Coarse-grained molecular dynamics simulations of membrane proteins: a practical guide.
In,
Schmidt-Krey, I. and Gumbart, J.C.
(eds.)
Structure and Function of Membrane Proteins.
(Methods in Molecular Biology, 2302)
New York.
Humana, .
(doi:10.1007/978-1-0716-1394-8_14).
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Book Section
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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e-pub ahead of print date: 21 April 2021
Published date: 2021
Additional Information:
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© 2021, Springer Science+Business Media, LLC, part of Springer Nature.
Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.
Keywords:
Membranes, Molecular dynamics, Molecular modelling, coarse-grained, membrane protein
Identifiers
Local EPrints ID: 449293
URI: http://eprints.soton.ac.uk/id/eprint/449293
PURE UUID: 4ad25ddc-3ff0-45f2-9c33-622df581672b
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Date deposited: 21 May 2021 16:33
Last modified: 17 Mar 2024 03:11
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Contributors
Author:
William G. Glass
Author:
Franca Fraternali
Author:
Irene Marzuoli
Author:
Marley Luke Samways
Author:
Philip C. Biggin
Author:
Syma Khalid
Editor:
I. Schmidt-Krey
Editor:
J.C. Gumbart
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