Abstract
Coarse-grained molecular dynamics (CGMD) simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances such as carbon nanotubes have been suggested. Here we briefly discuss a method for CGMD system configuration and the types of analysis and perturbations that can be performed with CGMD simulations. We also describe specific examples to show how CGMD simulations have been applied to various situations, and then describe experimental results that were used to validate the simulation results. CGMD simulations are applicable to resolving problems for various biological systems.
| Original language | English |
|---|---|
| Pages (from-to) | 1-15 |
| Number of pages | 15 |
| Journal | AIMS Biophysics |
| Volume | 1 |
| Issue number | 1 |
| DOIs | |
| Publication status | Published - 2014 |
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Keywords
- All atom-molecular dynamics
- Coarse-grained molecular dynamics
- In silico drug design
- Protein-lipid interactions
- Protein-protein interactions
- Reverse graining
ASJC Scopus subject areas
- Biophysics
- Structural Biology
- Molecular Biology
- Biochemistry
Cite this
Coarse-grained molecular dynamics simulations of biomolecules. / Takahashi, Ken; Oda, Takayuki; Naruse, Keiji.
In: AIMS Biophysics, Vol. 1, No. 1, 2014, p. 1-15.Research output: Contribution to journal › Review article
}
TY - JOUR
T1 - Coarse-grained molecular dynamics simulations of biomolecules
AU - Takahashi, Ken
AU - Oda, Takayuki
AU - Naruse, Keiji
PY - 2014
Y1 - 2014
N2 - Coarse-grained molecular dynamics (CGMD) simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances such as carbon nanotubes have been suggested. Here we briefly discuss a method for CGMD system configuration and the types of analysis and perturbations that can be performed with CGMD simulations. We also describe specific examples to show how CGMD simulations have been applied to various situations, and then describe experimental results that were used to validate the simulation results. CGMD simulations are applicable to resolving problems for various biological systems.
AB - Coarse-grained molecular dynamics (CGMD) simulations are increasingly being used to analyze the behaviors of biological systems. When appropriately used, CGMD can simulate the behaviors of molecular systems several hundred times faster than elaborate all-atom molecular dynamics simulations with similar accuracy. CGMD parameters for lipids, proteins, nucleic acids, and some artificial substances such as carbon nanotubes have been suggested. Here we briefly discuss a method for CGMD system configuration and the types of analysis and perturbations that can be performed with CGMD simulations. We also describe specific examples to show how CGMD simulations have been applied to various situations, and then describe experimental results that were used to validate the simulation results. CGMD simulations are applicable to resolving problems for various biological systems.
KW - All atom-molecular dynamics
KW - Coarse-grained molecular dynamics
KW - In silico drug design
KW - Protein-lipid interactions
KW - Protein-protein interactions
KW - Reverse graining
UR - http://www.scopus.com/inward/record.url?scp=85018215006&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85018215006&partnerID=8YFLogxK
U2 - 10.3934/biophy.2014.1.1
DO - 10.3934/biophy.2014.1.1
M3 - Review article
VL - 1
SP - 1
EP - 15
JO - AIMS Biophysics
JF - AIMS Biophysics
SN - 2377-9098
IS - 1
ER -