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Computers close in on protein structure prediction

and the protein backbone, the computer then uses a detailed physical chemistry based force field which favors close packing of atoms and hydrogen bonding to more accurately compute the energy of the structure.

"What seems to be critical is the packing of the molecule," Baker said. "The protein fits together perfectly with no holes in the middle, and no atoms on top of each other. It's about as densely packed as it could be. It's like a three-dimensional jigsaw puzzle."

The researchers upped their odds of finding the right match by repeating the two-step process with 50 homologs of the proteins from other genomes, such as a mouse or fly. The protocol was first tested on a blind annual prediction test considered to be the highest standard for removing bias from protein structure prediction models.

"We can't compute the energies perfectly, but the biggest problem is the search through possible shapes," Baker said. "Where we were not getting the right answer on the computer, it was almost always the case that the actual structure had the lowest energy, so we would have succeeded if we had explored this part of the space."

In a related paper published in the August issue of the journal Proteins, Baker and his colleagues reported that similar approaches can be used to predict the structures of protein complexes. "For the first time, computational methods are able, for a subset of cases, to produce really accurate models," he said.

Baker compares the computer simulations of the proteins to the problem of trying to find the lowest point on the surface of the Earth for the first time. A simple way to find the lowest place on the planet is to send out as many explorers as possible. The more explorers there are the more likely one of them is to stumble onto the shoreline of the Dead Sea ?the Earth's lowest point on land not covered by water. Each of the thousands of computer simulations is like one explorer.

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Source:Howard Hughes Medical Institute


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