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CG2AT2 : an enhanced fragment-based approach for serial multi-scale molecular dynamics simulations
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Vickery, Owen N. and Stansfeld, Phillip J. (2021) CG2AT2 : an enhanced fragment-based approach for serial multi-scale molecular dynamics simulations. Journal of Chemical Theory and Computation, 17 (10). pp. 6472-6482. doi:10.1021/acs.jctc.1c00295 ISSN 1549-9618.
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WRAP-CG2AT2-enhanced-fragment-based-approach-serial-multi-scale-molecular-dynamics-simulations-Stansfeld-2021.pdf - Published Version - Requires a PDF viewer. Available under License Creative Commons Attribution Non-commercial No Derivatives 4.0. Download (6Mb) | Preview |
Official URL: http://dx.doi.org/10.1021/acs.jctc.1c00295
Abstract
Coarse-grained molecular dynamics provides a means for simulating the assembly and interactions of macromolecular complexes at a reduced level of representation, thereby allowing both longer timescale and larger sized simulations. Here, we describe an enhanced fragment-based protocol for converting macromolecular complexes from coarse-grained to atomistic resolution, for further refinement and analysis. While the focus is upon systems that comprise an integral membrane protein embedded in a phospholipid bilayer, the technique is also suitable for membrane-anchored and soluble protein/nucleotide complexes. Overall, this provides a method for generating an accurate and well-equilibrated atomic-level description of a macromolecular complex. The approach is evaluated using a diverse test set of 11 system configurations of varying size and complexity. Simulations are assessed in terms of protein stereochemistry, conformational drift, lipid/protein interactions, and lipid dynamics.
Item Type: | Journal Article | ||||||||||||||||||||||||
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Subjects: | Q Science > QD Chemistry Q Science > QP Physiology |
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||||||||||||||||||||
Library of Congress Subject Headings (LCSH): | Molecular dynamics, Macromolecules, Membrane proteins, Phospholipids, Nucleotides, Stereochemistry | ||||||||||||||||||||||||
Journal or Publication Title: | Journal of Chemical Theory and Computation | ||||||||||||||||||||||||
Publisher: | American Chemical Society | ||||||||||||||||||||||||
ISSN: | 1549-9618 | ||||||||||||||||||||||||
Official Date: | 12 October 2021 | ||||||||||||||||||||||||
Dates: |
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Volume: | 17 | ||||||||||||||||||||||||
Number: | 10 | ||||||||||||||||||||||||
Page Range: | pp. 6472-6482 | ||||||||||||||||||||||||
DOI: | 10.1021/acs.jctc.1c00295 | ||||||||||||||||||||||||
Status: | Peer Reviewed | ||||||||||||||||||||||||
Publication Status: | Published | ||||||||||||||||||||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||||||||||||||||||||
Date of first compliant deposit: | 14 September 2021 | ||||||||||||||||||||||||
Date of first compliant Open Access: | 15 September 2021 | ||||||||||||||||||||||||
RIOXX Funder/Project Grant: |
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