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Computers close in on protein structure prediction

arable to what you can get by experiments."

The encouraging results come from a refinement of a sophisticated computer modeling program called Rosetta, first developed several years ago in Baker's lab. The program works on the premise that proteins collapse into their lowest energy state, like a ball that rolls down a hill until it comes to rest on level ground. The energies of hundreds of thousands of possible shapes generated by the computer are computed, and the lowest energy shape is selected as the prediction.

The prediction process happens in two steps, Bradley said. The first stage uses an approximate model which allows rapid calculation of the energy and so can be carried out rapidly, while the second uses a very detailed model for which the energy calculations take much longer but are much more accurate. A large scale search through possible structures is carried out in the first stage, and promising locations are then explored in detail in the second stage.

The first stage takes advantage of the fact that all amino acids have identical sections, which form the protein backbone. The computer adds a fuzzy picture of the protruding side chains that give each amino acid its unique identity. The sequence of side chains ultimately gives each protein its characteristic shape by the environment and neighbors they prefer.

Then the computer randomly twists, loops, and bends each amino acid sequence into 100,000 different shapes based on the preferred location of the amino acids. Some amino acids tend to dive toward the watery world of the protein surface while others take cover inside the protein. The computer also accounts for the social habits of the 20 amino acids; some want to be close to each other and others like their distance.

In stage two, Rosetta replaces the fuzzy picture of the side chains with detailed, physically realistic models with all the atoms represented. From the positions of the atoms in the sidechains
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Source:Howard Hughes Medical Institute


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