All Atom Protein Folding Simulations With Distributed Computational Resources
نویسندگان
چکیده
منابع مشابه
All-Atom Protein-Folding Simulations in Generalized-Ensembles
Because a protein is only functional if it folds into its characteristic shape, it is important to understand how the structure and the function of proteins emerge from their sequence of amino acids (the monomers of the linear chain that builds up a protein). Such knowledge could not only lead to the de novo design of proteins that serve as novel drugs with customized properties, but also to a ...
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Successful ab initio folding of proteins with both -helix and -sheet requires a delicate balance among a variety of forces in the simulation model, which may explain that the successful folding of any / proteins to within experimental error has yet to be reported. Here we demonstrate that it is an achievable goal to fold / proteins with a force field emphasizing the balance between the two majo...
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Advances in computing have enabled microsecond all-atom molecular dynamics trajectories of protein folding that can be used to compare with and test critical assumptions of theoretical models. We show that recent simulations by the Shaw group (10, 11, 14, 15) are consistent with a key assumption of an Ising-like theoretical model that native structure grows in only a few regions of the amino ac...
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We present an approach to predicting the folding time distribution from all-atom replica exchange simulations. This is accomplished by approximating the multidimensional folding process as stochastic reaction-coordinate dynamics for which effective drift velocities and diffusion coefficients are determined from the short-time replica exchange simulations. Our approach is applied to the folding ...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 2009
ISSN: 0006-3495
DOI: 10.1016/j.bpj.2008.12.3100