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Free‐energy‐driven folding and thermodynamics of the 67‐residue protein GS‐α 3 W—A large‐scale Monte Carlo study
Author(s) -
Meinke Jan H.,
Hansmann Ulrich H. E.
Publication year - 2009
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.21321
Subject(s) - monte carlo method , statistical physics , collision , protein folding , molecular dynamics , computer science , folding (dsp implementation) , physics , computational science , chemistry , computational physics , computational chemistry , mathematics , nuclear magnetic resonance , statistics , computer security , electrical engineering , engineering
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‐α 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. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009