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Computers close in on protein structure prediction

cent success rate reported in the Science paper might be good enough to secure hall-of-fame status for a baseball player, Baker is quick to point out that it is not yet reliable enough for biology. Better models will depend on both smarter exploration strategies and more computer power. "If methods stayed where we are, we wouldn't solve the problem," Baker said. "On the other hand, we would do better with 10 times more computer time."

It takes less than one minute for a protein to fold into its correct shape in cells, but one oft-repeated estimate predicts it would take longer than the age of the universe for a computer to sample all the possible confirmations of a folded protein. Baker's lab already receives help from supercomputing centers in San Diego and Illinois.

More help will soon be on its way from many of the 5,000 freshman entering University of Washington this fall. Using software developed to assist the Search for Extraterrestrial Intelligence (SETI) project, the students can put their computers to work at night while they are sleeping to search the atomic landscape for the lowest energy structure of proteins.

To improve protein structure prediction further, Baker's group has also started a distributed computing project that they are hoping will be aided by members of the public. The project, called Rosetta@home, is a scientific research project that uses internet-connected computers to predict and design protein structures, and protein-protein and protein-ligand interactions. The goal is to develop methods that accurately predict and design protein structures and complexes, an endeavor that may ultimately help researchers develop cures for human diseases such as cancer, HIV/AIDS, and malaria. More information is available online at http://boinc.bakerlab.org/rosetta.


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Source:Howard Hughes Medical Institute


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