Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

Atomistic simulations of protein folding have the potential to be a great complement to experimental studies, but have been severely limited by the time scales accessible with current computer hardware and algorithms. By employing a worldwide distributed computing network of tens of thousands of PCs and algorithms designed to efficiently utilize this new many-processor, highly heterogeneous, loosely coupled distributed computing paradigm, we have been able to simulate hundreds of microseconds of atomistic molecular dynamics. This has allowed us to directly simulate the folding mechanism and to accurately predict the folding rate of several fast-folding proteins and polymers, including a nonbiological helix, polypeptide alpha-helices, a beta-hairpin, and a three-helix bundle protein from the villin headpiece. Our results demonstrate that one can reach the time scales needed to simulate fast folding using distributed computing, and that potential sets used to describe interatomic interactions are sufficiently accurate to reach the folded state with experimentally validated rates, at least for small proteins. (C) 2002 Wiley Periodicals, Inc.
Publisher
JOHN WILEY & SONS INC
Issue Date
2003-01
Language
English
Keywords

MOLECULAR-DYNAMICS SIMULATIONS; BETA-HAIRPIN FORMATION; ENERGY LANDSCAPE; NONBIOLOGICAL HELIX; SECONDARY STRUCTURE; MOLTEN GLOBULE; TRANSITION; PATHWAYS; MODEL; KINETICS

Citation

BIOPOLYMERS, v.68, no.1, pp.91 - 109

ISSN
0006-3525
DOI
10.1002/bip.10219
URI
http://hdl.handle.net/10203/225426
Appears in Collection
CH-Journal Papers(저널논문)
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