ProteinQuest · a mode
BeadFold
In ProteinQuest you sorted building blocks into oily and watery. Here they are beads on a chain. In water, oily beads end up tucked against each other and watery beads end up on the outside. Fold the chain so as many oily beads touch as you can. Then try the hard way round: design a chain that folds into one shape and no other.
Toy model A simplified picture to show one idea. Not a measurement, and not a prediction. Of protein folding: two kinds of bead on a flat grid (the HP model), where real proteins have twenty kinds of building block and fold in 3D.
Oily bead (filled) Watery bead (open) two oily beads touching (not next to each other on the chain)
Fold it
Pick a chain. The first bead is placed for you. Tap a highlighted square (or use the arrow keys) to lay the next bead beside the last one. The chain cannot cross itself.
Design it
Here is a shape. Tap beads to make them oily or watery, then check: is this shape the one best fold of your chain? If another shape scores as well, or better, your chain is not designed yet.
Design is hard. Only 7 of the 256 possible 8-bead chains have one best fold at all, and between them they make just 5 of the 272 shapes an 8-bead chain can take. Real protein design, the work behind David Baker's share of the 2024 Nobel Prize in Chemistry, is the same question with twenty kinds of building block, in 3D.