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Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing
Author(s) -
Pande Vijay S.,
Baker Ian,
Chapman Jarrod,
Elmer Sidney P.,
Khaliq Siraj,
Larson Stefan M.,
Rhee Young Min,
Shirts Michael R.,
Snow Christopher D.,
Sorin Eric J.,
Zagrovic Bojan
Publication year - 2003
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.10219
Subject(s) - protein folding , molecular dynamics , folding (dsp implementation) , computer science , bundle , helix bundle , villin , computational science , chemistry , distributed computing , biological system , protein structure , computational chemistry , actin , materials science , biochemistry , composite material , electrical engineering , biology , engineering
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 α‐helices, a β‐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. © 2002 Wiley Periodicals, Inc. Biopolymers 68: 91–109, 2003