Two examples of how the protein structures predicted by Rosetta compare with the proteins' actual shapes. In both examples, the ab initio structure predicted by Rosetta is on the left, and the experimentally determined x-ray crystal structure is on the right. For clarity, the amino acid side chains are not shown and the protein backbone is colored to show the beginning and end of the chain. In both cases, the overall fold of the predicted structure is very similar to that of the native structure but has some details incorrect. The predictions provide valuable insights that are not evident from the proteins' amino acid sequences alone. When the protein predicted in the first example was compared with known protein structures in a database, for example, it closely resembled the structure of a protein that plays a role in killing bacteria. Sure enough, the predicted protein turned out to play a similar role, even though it has an unrelated amino acid sequence. The second example shows one domain of a large 811-residue protein that was found to resemble proteins with related functions but unrelated sequences.

Illustration: Rich Bonneau/Baker Lab

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