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Researcher laps drug treatment opponents

A KU researcher has beaten opponents by a wide margin in a competition that could lead to new drug treatments for various illnesses.

Yang Zhang, assistant professor of molecular biosciences, won first place in the prestigious automated server predictions category at the Critical Assessment of Structure Prediction competition.

Protein structures are 3-D illustrations of the amino acid sequences that make up a protein, or polypeptide chain, and give it its specific biological function.

"In order to know the function, we must know the structure, because the structure decides the function," Zhang said. "The final goal is we can design new drugs."

Finding the structure of a protein is a long, expensive process, said Zhang, also a faculty member at KU's Center for Bioinformatics. To identify one can cost nearly $1 million, and there is an infinite amount in nature. The international competition is "blind" because the protein structures are new, unpublished and therefore unknown.

To win the competition, which takes place biannually, Zhang's lab wrote a computer software program. The computer server generated the protein structure within the 48-hour time limit. Zhang's server is called the I-TASSER – Iterative Threading Assembly Refinement. It is a newer version of TASSER, which Zhang developed with Jeffrey Skolnick, a professor at the Georgia Institute of Technology.

Zhang competed against 98 others in the server competition.

The winners are selected by measuring their predictions against a structure created by a control group.

Zhang beat the second place winner by 5 percent to 10 percent.

"I'm happy that our method really worked well," he said. "Drug companies pay attention to the competition because if you win it, companies want to buy the software because these high-resolution protein models are very important to drug design."

This is the seventh year for the competition. Zhang was invited to speak at the Critical Assessment of Structure Prediction conference in California, Nov. 26-30.

Zhang has just completed his first year on the faculty at KU. Before coming to KU, he worked with Skolnick at the University at Buffalo.

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