![]() 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.Īs 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. The surface of the funnel is not smooth, having many hills and valleys. Diagrams of this type show a perspective view of a funnel or cone. The Foldit blog post "The problem of protein design" shows an example of a three-dimensional representation of a folding funnel. In an ideal folding funnel, the dots converge in a thin band toward the lower left corner of the plot. In Foldit, these solutions are collected automatically during gameplay. In a folding funnel plots, each dot represents a different solution or pose. 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. The concept of an energy landscape is often used in Foldit discussions, especially as it relates to protein design.įolding funnel diagrams offer one way of visualizing the energy landscape in two dimensions. Each green dot represents a player solution. The plots shows Foldit player solutions for Puzzle 689b: Hand-Folding CASP10 T0711 Repost. ![]() A "folding funnel" plot, showing RMSD on the horizontal X-axis, and free energy on the vertical Y-axis.
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