UW Today

This is an archived article.

February 24, 2005

Protein folding: DOE award will provide 2 million processor hours on supercomputer

Dr. Valerie Daggett, professor of medicinal chemistry in the School of Pharmacy, has received one of three Innovative and Novel Computational Impact on Theory and Experiment (INCITE) awards for her research in “molecular dynameomics.” This award, given by the U.S. Department of Energy (DOE) provides Daggett the use of 2 million processor hours on the DOE’s IBM supercomputer, housed at the National Energy Research Scientific Computing (NERSC) Center in Berkeley, Calif., to further her studies in protein folding with the aim of deciphering genetic information.

Daggett’s research focuses on realistic molecular modeling studies relating to protein stability, function and folding. She and her team of researchers use computer simulation methods to study the approximately 1,130 known, non-redundant protein folds. Up until this point, her team has been able to simulate about 30 of these folds. The supercomputer, which contains over 6,500 processors, will enable Daggett and her team to take their study to a new level. By running the hundreds upon hundreds of slightly different simulations supported by the supercomputer, Daggett will create an extensive repository of molecular dynamics structures for protein folds, including the unfolding pathways. In addition, the control native simulations will be used in drug design studies.

“We are excited about the massive resources to which we now have access,” says Daggett. “The supercomputer will enable us to do in a month and half what would take several lifetimes on a single processor.”

Although much is known of the structural details of the native folded conformation of proteins, very little is known about the actual folding process. An understanding of protein folding has important implications for all biological processes, including protein degradation, protein translocation, aging, and human diseases, including cancer and amyloid diseases.

Current market value for processing time is about $1 per hour. In addition to processing time, award winners will receive technical support and data storage privileges. This translates Daggett’s award to an equivalent value of well over $2 million. In addition to the DOE award, Daggett has recently received a $25,000 Microsoft SciData Award for an Internet-based protein simulation project.