Journal Article

PreJuSER-7200

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Free-energy-driven folding and thermodynamics of the 67-residue protein GS-alpha3W - A large-scale Monte Carlo study

Meinke, J. H.FZJ* ; Hansmann, U. H. E.

2009
Wiley New York, NY [u.a.]

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Please use a persistent id in citations: doi:10.1002/jcc.21321

Abstract: Utilizing the computational power of a few thousand processors on a BlueGene/P, we have explored the folding mechanism of the 67-residue protein GS-alpha(3)W. Results from our large-scale simulation indicate a diffusion-collision mechanism for folding. However, the lower-than-expected frequency of native-like configurations at physiological temperatures indicates shortcomings of our energy function. Our results suggest that computational studies of large proteins call for redevelopment and reparametrization of force fields that in turn require extensive simulations only possible with the newly available supercomputers with computing powers reaching the petaflop range.

Keyword(s): Computer Simulation (MeSH) ; Escherichia coli: genetics (MeSH) ; Models, Molecular (MeSH) ; Monte Carlo Method (MeSH) ; Protein Conformation (MeSH) ; Protein Folding (MeSH) ; Proteins: chemistry (MeSH) ; Thermodynamics (MeSH) ; Proteins ; J ; protein folding (auto) ; Monte Carlo simulation (auto) ; supercomputing (auto)

Note: The project was conceived and large part of the data collected while the authors were member of the "Computational Biology and Biophysics" group at the John von Neurriann Institute for Computing, Mich, Germany.

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Contributing Institute(s):

1. Jülich Supercomputing Centre (JSC)

Research Program(s):

1. Scientific Computing (P41)

Appears in the scientific report 2009

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