Shape Complementarity 01

Shape complementarity as seen in the Foldit objectives area. The value of -1 indicates the two protein chains are too far apart for shape complementarity to be calculated.

Shape complementarity is a measure of how of well the shapes of two proteins match each other at the interface between the proteins. Foldit binder puzzles may include a shape complementarity objective to help evaluate a binder design.

Shape complementarity is determined by mathematically comparing the shape of two proteins along the interface between them. The result is a unitless value which can range from 0.0 for a poor fit to 1.0 for a perfect fit. In practice, a value of 0.80 would indicate a very good fit.

Hovering over a calculated shape complementarity shows a suggested target. The initial puzzles have used a shape complementarity of 0.6 as a suggested goal.

When the two proteins are far apart, shape complementarity may show a value of -1, which is basically an error code, indicating that a reasonable calculation is not possible. The binder may be too far away from the target, or the interface may be too small for a meaningful result. The -1 value may be seen when first opening a design puzzle, when the designable section appears as an extended chain.

Shape complementarity is described further in the Foldit blog post Analysis of Protein Binder Designs.

As of its initial release in August 2020, shape complementarity scoring in Foldit is very slow to calculate. A binder puzzle may have a "shape complementarity" objective, but players must click "run" or "run all" to see its value. There is no "enable" checkbox, meaning the shape complementarity score won't be calculated automatically with the other scores. At this stage, the shape complementarity score is for information only, and does not affect the Foldit score.

The Foldit developers are planning a feature which would allow calculating shape complementarity asynchronously, meaning without affecting interface gameplay. The initial version of shape complementarity causes a delay of several seconds while calculating, effectively causing Foldit to freeze until the calculation finishes.

Shape complementarity first appeared as an objective in Puzzle 1054 Vancomycin Binder: Shape Complementarity back in 2015. (See Puzzle 1054 results.) In puzzle 1054, the shape complementarity objective awarded a bonus of up to 1500 points.

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