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

摘要: Atomistic simulations of protein folding have the potential to be a great complement experimental studies, but been severely limited by time scales accessible with current computer hardware and algorithms. By employing worldwide distributed computing network tens thousands PCs algorithms designed efficiently utilize this new many-processor, highly heterogeneous, loosely coupled paradigm, we able simulate hundreds microseconds atomistic molecular dynamics. This has allowed us directly mechanism accurately predict rate several fast-folding proteins polymers, including nonbiological helix, polypeptide α-helices, β-hairpin, three-helix bundle from villin headpiece. Our results demonstrate that one can reach needed fast using computing, sets used describe interatomic interactions are sufficiently accurate folded state experimentally validated rates, at least for small proteins. © 2002 Wiley Periodicals, Inc. Biopolymers 68: 91–109, 2003