A review of coarse-grained molecular dynamics techniques to access extended spatial and temporal scales in biomolecular simulations

BA Merchant, JD Madura - Annual Reports in Computational Chemistry, 2011 - Elsevier
The study of very large biomolecular systems over extended spatial and temporal scales is
being accomplished through the use of coarse-grained (CG) models. The successes of …

Coarse-grained molecular simulations of large biomolecules

S Takada - Current opinion in structural biology, 2012 - Elsevier
Recently, we saw a dramatic increase in the number of researches that rely on coarse-
grained (CG) simulations for large biomolecules. Here, first, we briefly describe recently …

[HTML][HTML] Coarse-grained molecular dynamics simulations of biomolecules

K Takahashi, T Oda, K Naruse - AIMS Biophysics, 2014 - aimspress.com
Coarse-grained molecular dynamics (CGMD) simulations are increasingly being used to
analyze the behaviors of biological systems. When appropriately used, CGMD can simulate …

Highly scalable and memory efficient ultra-coarse-grained molecular dynamics simulations

JMA Grime, GA Voth - Journal of chemical theory and computation, 2014 - ACS Publications
The use of coarse-grained (CG) models can significantly increase the time and length scales
accessible to computational molecular dynamics (MD) simulations. To address very large …

Modeling structural dynamics of biomolecular complexes by coarse-grained molecular simulations

S Takada, R Kanada, C Tan, T Terakawa… - Accounts of chemical …, 2015 - ACS Publications
Conspectus Due to hierarchic nature of biomolecular systems, their computational modeling
calls for multiscale approaches, in which coarse-grained (CG) simulations are used to …

A review of advancements in coarse-grained molecular dynamics simulations

SY Joshi, SA Deshmukh - Molecular Simulation, 2021 - Taylor & Francis
Over the last few years, coarse-grained molecular dynamics has emerged as a way to model
large and complex systems in an efficient and inexpensive manner due to its lowered …

Backmapping from multiresolution coarse-grained models to atomic structures of large biomolecules by restrained molecular dynamics simulations using bayesian …

J Peng, C Yuan, R Ma, Z Zhang - Journal of chemical theory and …, 2019 - ACS Publications
Coarse-grained (CG) simulations have allowed access to larger length scales and longer
time scales in the study of the dynamic processes of large biomolecules than all-atom (AA) …

The power of coarse graining in biomolecular simulations

HI Ingólfsson, CA Lopez, JJ Uusitalo… - Wiley …, 2014 - Wiley Online Library
Computational modeling of biological systems is challenging because of the multitude of
spatial and temporal scales involved. Replacing atomistic detail with lower resolution …

Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS

V Niranjan, P Rao, A Uttarkar, J Kumar - Plos one, 2023 - journals.plos.org
Coarse-grained simulations have emerged as a valuable tool in the study of large and
complex biomolecular systems. These simulations, which use simplified models to represent …

Recent advances in transferable coarse-grained modeling of proteins

P Kar, M Feig - Advances in protein chemistry and structural biology, 2014 - Elsevier
Computer simulations are indispensable tools for studying the structure and dynamics of
biological macromolecules. Biochemical processes occur on different scales of length and …