Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications

International Journal of Molecular Sciences
Nidhi Singh, Wenjin Li

Abstract

Molecular dynamics simulations have emerged as a powerful tool to study biological systems at varied length and timescales. The conventional all-atom molecular dynamics simulations are being used by the wider scientific community in routine to capture the conformational dynamics and local motions. In addition, recent developments in coarse-grained models have opened the way to study the macromolecular complexes for time scales up to milliseconds. In this review, we have discussed the principle, applicability and recent development in coarse-grained models for biological systems. The potential of coarse-grained simulation has been reviewed through state-of-the-art examples of protein folding and structure prediction, self-assembly of complexes, membrane systems and carbohydrates fiber models. The multiscale simulation approaches have also been discussed in the context of their emerging role in unravelling hierarchical level information of biosystems. We conclude this review with the future scope of coarse-grained simulations as a constantly evolving tool to capture the dynamics of biosystems.

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Citations

Aug 11, 2020·The Journal of Chemical Physics·Beytullah Ozgur, Mehmet Sayar
Nov 14, 2019·International Journal of Molecular Sciences·Nandhini RajagopalShikha Nangia
Jul 14, 2020·Frontiers in Bioengineering and Biotechnology·Konda Mani SaravananYanjie Wei
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Apr 30, 2021·Journal of Chemical Theory and Computation·Christos LamprakisZoe Cournia
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Sep 25, 2021·Journal of Chemical Information and Modeling·Cristina González-FernándezInmaculada Ortiz
May 17, 2021·Molecular Metabolism·Michael C Lawrence
Oct 14, 2021·Journal of the American Chemical Society·Ping GaoTâp Ha-Duong

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Methods Mentioned

BETA
protein folding
peptide folding
acetylation

Software Mentioned

UNRES
OPEP
flex
PRIMO
HOOMD
ESPResSO
LAMMPS
MARTINI
CABS
CHARMM

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