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Folding probabilities: A novel approach to folding transitions and the two-dimensional Ising-model
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26.The fact that the formation of helices can be reasonably well characterized by the reaction coordinate ξ is a consequence from the one-dimensional nature of this structure. However, this approach cannot be easily generalized to the folding of more complex proteins.
27.Again, one should note the big advantage of our approach as compared with the direct calculation of We are able to achieve the same accuracy by analyzing only 466 runs instead of 9900 runs.
28.This statement is supported by our analysis of a simple MD model for protein folding (data not shown). In these MD simulations, phase space is explored much more thoroughly and the various protein configurations are much more connected. As a consequence, the folding probability of the protein configurations is generally much smaller than in the MC model and only weakly depends on the order parameter.
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