University of Michigan lab takes top honours in worldwide protein prediction competition

The University of Michigan Health System took top honours in the Critical Assessment of Techniques for Protein Structure Prediction, a biennial scientific competition to test protein structure and function prediction methods developed by laboratories all over the world.

The U-M lab of Yang Zhang, Ph.D., was ranked No. 1 in both protein structure and function prediction among more than 200 groups.

Understanding the role of protein molecules is vital for health research and finding cures and medicines for diseases. The human body has about a million different protein molecules, which serve to manipulate and accommodate important cellular procedures, such as metabolism, signalling cell structures, hormone action and cell-to-cell interactions.

Many common diseases, including cancer, diabetes and obesity, may be treated or cured by designing drugs that can activate or inhibit corresponding protein molecules.

The winning team included Zhang, graduate student Ambrish Roy, and postdoctoral fellows, Dong Xu, Ph.D., and Jian Zhang, Ph.D. Zhang’s lab also won CASP protein structure prediction competitions in 2006 and 2008.

“CASP is the Olympics of protein science, and Zhang is like a three-time Olympic champion,” offers Gilbert S. Omenn , M.D., Ph.D., director of the U-M Center for Computational Medicine and Bioinformatics.

For the competition, scientists were given the amino acid sequence of more than 100 unknown proteins and directed to predict what the detailed three-dimensional shape of each protein is and what the molecule does in living cells.

The ability to predict the three-dimensional protein structure from amino acid sequence by computer is extremely helpful to health research and the drug-discovery industry, and could make research more cost-effective.

“Many proteins, especially those embedded in the cell membrane, are difficult or even impossible to solve using current experimental techniques,” says Zhang, associate professor of computational medicine and bioinformatics at the U-M Medical School. “Computational methods provide a possible avenue to deal with these molecules.”

The main focus of Zhang’s U-M lab is to develop computer algorithms to predict three-dimensional structures of protein molecules from amino acid sequences.

Approximately 15,000 registered scientists from 89 countries use the lab’s on-line system and algorithms to generate protein structure and function modelling for their own research.