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Coarse-grained molecular dynamics simulations of membrane proteins: a practical guide

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
Humana
Glass, William G.
b94d3b90-0e95-4dcd-88f6-bfc2295e3b13
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Fraternali, Franca
28f6ff16-64de-406c-ac25-728eaf65c8c9
Marzuoli, Irene
2aad03e4-78c9-43aa-806e-b7c9ca75ca6e
Samways, Marley Luke
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Biggin, Philip C.
c7394f79-450a-46c6-b77a-fadac30ded33
Khalid, Syma
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Schmidt-Krey, I.
Gumbart, J.C.
Glass, William G.
b94d3b90-0e95-4dcd-88f6-bfc2295e3b13
Essex, Jonathan W.
1f409cfe-6ba4-42e2-a0ab-a931826314b5
Fraternali, Franca
28f6ff16-64de-406c-ac25-728eaf65c8c9
Marzuoli, Irene
2aad03e4-78c9-43aa-806e-b7c9ca75ca6e
Samways, Marley Luke
75cda5aa-31ef-4f62-9ea3-8655ea55d3fb
Biggin, Philip C.
c7394f79-450a-46c6-b77a-fadac30ded33
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Schmidt-Krey, I.
Gumbart, J.C.

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, pp. 253-273. (doi:10.1007/978-1-0716-1394-8_14).

Record type: 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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More information

e-pub ahead of print date: 21 April 2021
Additional Information: Publisher Copyright: © 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
ORCID for Jonathan W. Essex: ORCID iD orcid.org/0000-0003-2639-2746
ORCID for Marley Luke Samways: ORCID iD orcid.org/0000-0001-9431-8789
ORCID for Syma Khalid: ORCID iD orcid.org/0000-0002-3694-5044

Catalogue record

Date deposited: 21 May 2021 16:33
Last modified: 26 Nov 2021 03:12

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Contributors

Author: William G. Glass
Author: Franca Fraternali
Author: Irene Marzuoli
Author: Marley Luke Samways ORCID iD
Author: Philip C. Biggin
Author: Syma Khalid ORCID iD
Editor: I. Schmidt-Krey
Editor: J.C. Gumbart

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