2002/12/02 by Vijay S. Pande, Ian S. Baker, Jarrod Chapman +8 · 8 citations
Biochemistry, Genetics and Molecular Biology · Materials Science · Chemistry · #Protein Structure and Dynamics #Enzyme Structure and Function #RNA and protein synthesis mechanisms #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
paper · doi:10.1002/bip.10219
openalex publication_date 2002/12/02 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.