A "folding funnel" plot, showing RMSD on the horizontal X-axis, and free energy on the vertical Y-axis. The plots shows Foldit player solutions for Puzzle 689b: Hand-Folding CASP10 T0711 Repost. Each green dot represents a player solution.

The concept of an energy landscape is often used in Foldit discussions, especially as it relates to protein design.

Folding funnel diagrams offer one way of visualizing the energy landscape in two dimensions. These diagrams plot the differences between different folds of a protein, with RMSD distance on the horizontal X-axis, and free energy (closely related to the score in Foldit) on the vertical Y-axis.

In a folding funnel plots, each dot represents a different solution or pose. In Foldit, these solutions are collected automatically during gameplay.

In an ideal folding funnel, the dots converge in a thin band toward the lower left corner of the plot.

The Foldit blog post "The problem of protein design" shows an example of a three-dimensional representation of a folding funnel. Diagrams of this type show a perspective view of a funnel or cone. The surface of the funnel is not smooth, having many hills and valleys. The neck of the funnel or the point of the cone is expected to be the native solution for the protein, the one with the lowest free energy.

As the "The problem of protein design" explains, while these 2D and 3D representations can be helpful, they don't really do justice to the full complexity of the energy of the landscape. Even for a 65-segment protein, 130 dimensions would be needed for a full picture.

See also these Foldit blog posts:

Community content is available under CC-BY-SA unless otherwise noted.