Ying Xu
  News-Sentinel photo by Michael Patrick

RNL scientist Ying Xu uses computers to help predict the three-dimensional structure of proteins.

from Knoxville News-Sentinel
October 21, 2002
original URL: http://www.knoxnews.com/kns/ornl/article/0,1406,KNS_4257_1484537,00.html

In biology, proteins are a key

Powerful processors enable 100-year simulations of physical conditions from mountains to oceans

By Frank Munger, News-Sentinel senior writer
October 21, 2002

In computational biology, function follows form.

By using computers to accurately predict the structure of proteins, scientists can better understand how these substances carry out their jobs inside cells and make the human body work. That information then can be used to figure out ways to alter protein functions when the body isn't working properly.

"One application of our work is to do drug design," said Ying Xu, who heads an Oak Ridge research group that uses both supercomputers and computer cluster groups to simulate the three-dimensional structure of proteins.

Xu describes it as a lock-and-key process.

If researchers identify the structure of a disease-causing protein, they can design a drug that will attach itself like a key in a lock, unleashing a chemical reaction that kills the virus or bacteria.

The Oak Ridge team is working with the Southeastern Structural Genomics Consortium, based at the University of Georgia, to identify proteins of priority for additional study.

An estimated 100,000 proteins exist to perform tasks assigned by one's genetic blueprint.

"Protein structure is the key to understanding protein function. If we can make a structural prediction accurately, it will help a lot with the functional study," said Xu, who received his doctorate in computer science from the University of Colorado.

He joined the staff at Oak Ridge National Laboratory about 10 years ago.

Xu's research group is among the best at predicting protein structures, finishing sixth in an international competition two years ago. The predicted structures are compared with the actual structures that previously have been determined, but not published, with experiments using techniques such as x-ray crystallography.

The Oak Ridge scientists are awaiting the results from the latest competition, the Critical Assessment of Techniques for Protein Structure Prediction. It was conducted from May to September.

"I think we can probably do better this year," Xu said.

The researchers developed a program called PROSPECT (Protein Structure Prediction and Evaluation Computer Toolkit), which makes highly detailed predictions based on known structures identified through experiments.

The software evaluates the possible structural alignments of amino acids that form proteins against known templates, using the sequencing information that is available to determine the best "fit."

Xu said scientists use different versions of PROSPECT depending on whether they're working on one of the lab's supercomputers or an experimental cluster of PCs, such as the 64-node cluster in the Center for Computational Sciences.

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