Professor Vijay Pande
Department of Chemistry
Stanford, University
Stanford, California
Folding@home

Monday, April 15, 2002
3:00 pm (CT)
3269 Beckman Institute

Abstract

Atomistic simulations of protein folding have the potential to be a great complement to experimental studies, but have been severely limited by the timescales accessible by current computer hardware and algorithms. By employing a worldwide distributed computing network of over a hundred thousand PCs ("Folding@Home") and algorithms designed to efficiently utilize this new large-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 non-biological helix, polypeptide alpha helices, a beta hairpin, beta-beta-alpha fold, and a three helix bundle protein from the villin headpiece. Our results demonstrate that one can reach the timescales needed to simulate fast folding using distributed computing, and that potential sets used to describe inter-atomic interactions appear to be sufficiently accurate to reach the folded state with experimentally validated rates, at least for small proteins.

Tea and coffee will be served in R3151 Beckman Institute at 2:15pm.