Folding funnel 2005789 0

An early result from the 2018 Protein Design Partition Tournament. The player-designed protein turned out to have multiple decoy states. Colored dots show the decoys in the plot on the left, and corresond to the colored bars in the graph on the right. (Click for larger image.)

A decoy is a solution to a protein that has low free energy (in Foldit, a high score), but is not close to the known native shape or the desired design shape.

Decoys are also referred to as "holes" in the "energy landscape" of a protein. In Foldit or in a folding simulation such as Rosetta@Home, a protein can get stuck in one of these holes. The only way out of a hole is to increase free energy (lower the Foldit score), change the shape of the protein, and try again.

A plot called a folding funnel can be used to illustrate decoys. Ideally, a folding funnel has a thin neck pointing to the lower left corner of the plot. This indicates the solutions are converging toward a reference solution, such as a known native.

Decoys are points that are close to horizontal X-axis of the folding funnel, indicating low free energy. Decoys that are close to the vertical Y-axis are close to the shape of the reference solution, so they're less of a concern. The farther away the decoy is from the Y-axis, the more likely it is to be a problem.

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