Folding@Home: Can a grid of 100,000 CPUs tackle fundamental barriers in molecular simulation?

Molecular simulation is greatly restricted by the limitations of modern computer power. Indeed, accurate, atomic-level simulation of the folding of proteins or the free energy of drug binding would require hundreds of years on the fastest computers. By coupling novel grid-computing algorithms and over 100,000 CPUs located throughout the world, the Folding@Home project (http://folding.stanford.edu) has been able to make significant advances in molecular simulation, including the first simulations of protein folding in full atomic detail with quantitative agreement with experiment as well as high precision free energy calculation. Finally, applications of this technology to the study of disease, including Alzheimer’s Disease, cancer, and Osteogenesis Imperfecta will be discussed.

Presenter(s)

Professor Pande's current research centers on the development and application of novel grid computing simulation techniques to address problems in chemical biology. In particular, he has pioneered novel distributed computing methodology to break fundamental barriers in the simulation of kinetics and thermodynamics of proteins and nucleic acids. As director of the Folding@Home and Genome@Home projects (http://folding.stanford.edu), Prof. Pande has, for the first time, directly simulated protein folding dynamics with quantitative comparisons with experiment, often considered a ³holy grail² of computational biology. His current research also includes novel simulation methods for high precision drug binding affinity calculations, protein design, and synthetic bio-mimetic polymers.

Prof. Pande received a BA in Physics at Princeton University in 1992. There, he was first introduced to biophysical questions, especially in his undergraduate thesis research with Prof. Philip Anderson, a Nobel Laureate in physics. Three years later, he received his Ph.D. in Physics from MIT, studying as a NSF Fellow under Profs. Toyoichi Tanaka and Alexander Grosberg. At MIT, Prof. Pande's research centered on statistical mechanical models of protein folding and design, suggesting novel ways to design protein sequences to have the desired stability and folding properties. As a Miller Fellow working with Prof. Daniel Rokhsar at UC Berkeley, Prof. Pande extended this methodology to examine atomistic protein models. Prof. Pande has won numerous awards, including most recently being named to MIT's TR100 (top young innovators in 2002), a Frederick E. Terman Fellowship (2002), and a Henry and Camile Dreyfus Teacher-Scholar (2003). Prof. Pande is currently an Assistant Professor of Chemistry and (by courtesy) of Structural Biology.