Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-Bath dynamics and tests on model alpha-helical systems

Article Abstract:

A study introduces the Langevin dynamics with the united-residue (UNRES) force field to take into account the dynamic effects of the solvent. It is found that the UNRES time scale is 4 times longer than that of all-atom molecular dynamics simulations because the degrees of freedom corresponding to the fastest motions in UNRES are averaged out.

Polypeptides, Structure, Heavy ions

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Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and test of the optimization method with single training proteins

Article Abstract:

Study is presented on the modification and parametrization of the united-residue (UNRES) force field for energy-based protein structure prediction and protein folding simulations. Result demonstrates that it is possible to optimize the UNRES force field for canonical simulations using a protein of any type of secondary structure.

Protein folding

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Molecular dynamics with the united-residue force field: Ab initio folding simulations of multichain proteins

Article Abstract:

Molecular dynamics is implemented with united-residue (UNRES) force field to treat multichain proteins. Simulations are carried out for both isolated single chains and the multichain complexes.

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