Pittsburgh Supercomputing Center

FOR IMMEDIATE RELEASE                         CONTACT:
May 4, 1999                                        Michael Schneider
                                                   Pittsburgh Supercomputing Center
                                                   (412) 268-4960

Protein Research at PSC is Finalist for Science Award

Longest-Ever Simulation of Protein Folding Gives New Insight

PITTSBURGH — Research at the Pittsburgh Supercomputing Center on how a newborn protein changes into its mature shape is a finalist for the 1999 Computerworld Smithsonian Award in Science. The project — a collaboration between PSC and Peter Kollman and Yong Duan of the University of California, San Francisco — is the longest-ever simulation of the folding action of a protein.

The "protein-folding problem," as it is called by scientists, addresses the question of how in the first few microseconds of its existence a protein transforms from a stretched-out chain of amino acids to a folded structure. Only in its final shape, usually a bundle of complex twists, turns and helices, can a protein do its biological job. If scientists can learn the rules governing the folding process, it will be possible in theory to design drugs for particular tasks. Recent research, for instance, suggests that certain diseases, such as "mad cow" and Alzheimer's disease, are malfunctions in protein folding, which could be amenable to drug therapy.

Scientists have used powerful computers to simulate these folding processes. Such studies helped develop new cancer drugs, for instance, but the studies are severely limited by the huge amount of computing time required. Kollman and Duan developed improved protein-simulation software that can exploit massively parallel systems, like the CRAY T3D and CRAY T3E at Pittsburgh, much more effectively than before.

Using this software, and computing resources at Pittsburgh and at Cray Research, Duan and Kollman simulated the folding of a small protein in water for a full microsecond, 100 times longer than prior similar simulations. The results, reported in SCIENCE — the leading U.S. scientific journal — offer new insight into the folding process.

More information, including graphics, about this research is available at: http://www.psc.edu/science/kollman98.html

Sponsored by Computerworld magazine and the Smithsonian Institution, the annual Computerworld Smithsonian awards honor innovative efforts that use information technology to improve human life. The protein-folding simulation is one among five projects chosen nationally as finalists for the CWSA science award. The winning projects will be announced at a gala dinner, June 7, at the National Building Museum in Washington, DC.

The Pittsburgh Supercomputing Center has been a finalist or winner of the CWSA award in Science six of the past seven years.

The Pittsburgh Supercomputing Center is operated by Carnegie Mellon University in consultation with the University of Pittsburgh and with the assistance of Westinghouse Electric Company. It was established in 1986 and is supported by several federal agencies, the Commonwealth of Pennsylvania and private industry.

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Revised: May 4, 1999

URL: http://www.psc.edu/publicinfo/news/1999/protein_05-04-1999.html