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Bottom-up coarse-graining: Principles and perspectives
Large-scale computational molecular models provide scientists a means to investigate the
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …
effect of microscopic details on emergent mesoscopic behavior. Elucidating the relationship …
General patchy ellipsoidal particle model for the aggregation behaviors of shape-and/or surface-anisotropic building blocks
ZW Li, YL Zhu, ZY Lu, ZY Sun - Soft Matter, 2018 - pubs.rsc.org
We present a general patchy ellipsoidal particle model suitable for conducting dynamics
simulations of the aggregation behaviors of various shape-and/or surface-anisotropic …
simulations of the aggregation behaviors of various shape-and/or surface-anisotropic …
Coarse-Grained modeling of nucleic acids using anisotropic Gay–Berne and electric multipole potentials
G Li, H Shen, D Zhang, Y Li… - Journal of Chemical Theory …, 2016 - ACS Publications
In this work, we attempt to apply a coarse-grained (CG) model, which is based on
anisotropic Gay–Berne and electric multipole (EMP) potentials, to the modeling of nucleic …
anisotropic Gay–Berne and electric multipole (EMP) potentials, to the modeling of nucleic …
Anisotropic coarse-grained model for proteins based on Gay–Berne and electric multipole potentials
H Shen, Y Li, P Ren, D Zhang, G Li - Journal of chemical theory …, 2014 - ACS Publications
Gay–Berne anisotropic potential has been widely used to evaluate the nonbonded
interactions between coarse-grained particles being described as elliptical rigid bodies. In …
interactions between coarse-grained particles being described as elliptical rigid bodies. In …
Physics-based potentials for the coupling between backbone-and side-chain-local conformational states in the united residue (UNRES) force field for protein …
The UNited RESidue (UNRES) model of polypeptide chains is a coarse-grained model in
which each amino-acid residue is reduced to two interaction sites, namely, a united peptide …
which each amino-acid residue is reduced to two interaction sites, namely, a united peptide …
Effect of disulfide bridge on the binding of SARS-CoV-2 fusion peptide to cell membrane: a coarse-grained study
H Shen, Z Wu - ACS omega, 2022 - ACS Publications
In this paper, we present the parameterization of the CAVS coarse-grained (CG) force field
for 20 amino acids, and our CG simulations show that the CAVS force field could accurately …
for 20 amino acids, and our CG simulations show that the CAVS force field could accurately …
A review of physics-based coarse-grained potentials for the simulations of protein structure and dynamics
H Shen, Z ** scheme
X Li, L Gao, W Fang - PLoS One, 2016 - journals.plos.org
In this article, a new set of parameters compatible with the dissipative particle dynamics
(DPD) force field is developed for phospholipids. The coarse-grained (CG) models of these …
(DPD) force field is developed for phospholipids. The coarse-grained (CG) models of these …