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Protein folding dynamic Monte Carlo simulation

Skolnick, J, Kolinski, A Dynamics monte carlo simulations of a new lattice model of globular protein folding, structure and dynamics J. Mol. Biol. 1991 221, 499-531. [Pg.652]

J. Skolnick and A. Kolinski, J. Mol. Biol., 212, 787 (1990). Dynamic Monte Carlo Simulations of Globular Protein Folding/Unfolding Pathways. I. Six-Member, Greek Key Beta-Barrel Proteins. [Pg.79]

In summary, the recent developments allow Monte Carlo simulations of protein dynamics in their denatured state, in the intermediate states and in the folded state. In the latter case, where the fine details are of major interest, standard MD techniques are usually superior to the Monte Carlo reduced model approaches. [Pg.208]

The two-dimensional square lattice protein folding model discussed earlier provides a simple basis for probing this issue. The model has the advantage of allowing one to carry out many exact calculations to check the predictions from first-order sensitivity theory. Unlike molecular dynamics or Monte Carlo simulations, there are no statistical errors or convergence problems associated with the calculations of the properties, and their parametric derivatives, of a model polypeptide on a two-dimensional square lattice. [Pg.307]

To study protein folding theoretically, simulation methods have proved indispensable. The folding transition is ultimately governed by statistical thermodynamics and hence it is paramount to use sampling methods that are able to reproduce the canonical Boltzmann distribution. Common sampling techniques are molecular dynamics (MD), Langevin or Brownian dynamics (BD) and Monte Carlo (MC). [Pg.403]

The feedback-optimized parallel tempering technique [26] outlined in the previous section has recently been applied to study the folding of the 36-residue chicken villin headpiece sub-domain HP-36 [27]. Since HP-36 is one of the smallest proteins with well-defined secondary and tertiary structure [28] and at the same time with 596 atoms still accessible to numerical simulations, it has recently attracted considerable interest as an example to test novel numerical techniques, including molecular dynamics [29,30] and Monte Carlo [31,32] methods. The experimentally determined structure [28] which is deposited in the Protein Data Bank (PDB code Ivii) is illustrated in the left panel of Fig. 6. [Pg.611]


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