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) …

A systematic methodology for defining coarse-grained sites in large biomolecules

Z Zhang, L Lu, WG Noid, V Krishna, J Pfaendtner… - Biophysical journal, 2008 - cell.com
Coarse-grained (CG) models of biomolecules have recently attracted considerable interest
because they enable the simulation of complex biological systems on length-scales and …

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 …

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 …

Reconstructing atomistic detail for coarse-grained models with resolution exchange

P Liu, Q Shi, E Lyman, GA Voth - The Journal of chemical physics, 2008 - pubs.aip.org
Coarse-grained (CG) modeling has emerged as a promising tool to bridge the gap between
the temporal and spatial scales of all-atom (AA) simulations and those of many important …

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 …

CG2AA: backmapping protein coarse-grained structures

LE Lombardi, MA Martí, L Capece - Bioinformatics, 2016 - academic.oup.com
Coarse grain (CG) models allow long-scale simulations with a much lower computational
cost than that of all-atom simulations. However, the absence of atomistic detail impedes the …

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 …

[HTML][HTML] Magic v. 3: An integrated software package for systematic structure-based coarse-graining

A Mirzoev, L Nordenskiöld, A Lyubartsev - Computer Physics …, 2019 - Elsevier
Molecular simulations of many phenomena related to biomolecular systems, soft matter and
nanomaterials require consideration of length scales above 10 nm and time scales longer …

Implementation of residue-level coarse-grained models in GENESIS for large-scale molecular dynamics simulations

C Tan, J Jung, C Kobayashi, DUL Torre… - PLOS Computational …, 2022 - journals.plos.org
Residue-level coarse-grained (CG) models have become one of the most popular tools in
biomolecular simulations in the trade-off between modeling accuracy and computational …