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Molecular Dynamics Simulations
Current Opinion in Structural Biology, 2002Molecular dynamics simulations have become a standard tool for the investigation of biomolecules. Simulations are performed of ever bigger systems using more realistic boundary conditions and better sampling due to longer sampling times. Recently, realistic simulations of systems as complex as transmembrane channels have become feasible.
Daan Frenkel, Berend Smit
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2012
Molecular dynamics (MD) simulation holds the promise of revealing the mechanisms of biological processes in their ultimate detail. It is carried out by computing the interaction forces acting on each atom and then propagating the velocities and positions of the atoms by numerical integration of Newton's equations of motion.
Xiaolin, Cheng, Ivaylo, Ivanov
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Molecular dynamics (MD) simulation holds the promise of revealing the mechanisms of biological processes in their ultimate detail. It is carried out by computing the interaction forces acting on each atom and then propagating the velocities and positions of the atoms by numerical integration of Newton's equations of motion.
Xiaolin, Cheng, Ivaylo, Ivanov
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Phys. Chem. Chem. Phys., 2014
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Ashfold, M. N. R., Parker, D. H.
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Ashfold, M. N. R., Parker, D. H.
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Application of molecular dynamics simulation in biomedicine
Chemical Biology and Drug Design, 2022Molecular dynamics (MD) simulation has been widely used in the field of biomedicine to study the conformational transition of proteins caused by mutation or ligand binding/unbinding.
Xiaodong Wu, Li-Yan Xu, E. Li, Geng Dong
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Molecular Dynamics of Acetylcholinesterase
Accounts of Chemical Research, 2002Molecular dynamics simulations are leading to a deeper understanding of the activity of the enzyme acetylcholinesterase. Simulations have shown how breathing motions in the enzyme facilitate the displacement of substrate from the surface of the enzyme to the buried active site.
Shen, Tongye +3 more
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Nonequilibrium Molecular Dynamics
Annual Review of Physical Chemistry, 1983Abstract MOLECULAR DYNAMICS has been generalized in order to stimulate a variety of NONEQUILIBRIUM systems. This generalization has been achieved by adopting microscopic mechanical definitions of macroscopic thermodynamic and hydrodynamic variables, such as temperature and stress. Some of the problems already treated include rapid plastic deformation,
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