Coarse-grained molecular dynamics simulations of biomolecules

Research output: Contribution to journalReview article

5 Citations (Scopus)

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 languageEnglish
Pages (from-to)1-15
Number of pages15
JournalAIMS Biophysics
Volume1
Issue number1
DOIs
Publication statusPublished - 2014

Fingerprint

Biomolecules
Molecular Dynamics Simulation
Molecular dynamics
Computer simulation
Biological systems
Carbon Nanotubes
Nucleic Acids
Dynamical systems
Lipids
Atoms

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 journalReview article

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