Docking Design is a beginner puzzle. It's an example of one type of design puzzle found in Foldit.
This puzzle has two pieces. There's a small section of protein that can be designed. The much larger section of protein is locked, preventing you from mutating any segments. The backbone shape of the locked section also can't be changed, but many of the sidechains in the locked section can move to new positions.
The goal of this puzzle is to design the small section to bond to a specific spot on the larger protein target. A successful design could be used to develop new drugs or biological therapies for conditions related to the large protein.
If you move the design section too far from the main protein, red constraints appear. The constraints act like bands, pulling the design section toward the target when you wiggle the protein. You can also use the move tool to adjust the position of the design section.
Tools and strategiesEdit
The design section is all isoleucine at the start of the puzzle.
To get started, you can try to mutate all segments. In the original interface, use the keyboard shortcut M (lowercase "m") or select "Mutate" from the Actions menu. In the selection interface, use the mutate icon or the Y (lowercase "y") keyboard shortcut. After mutating, shake and wiggle. You can repeat mutate, shake, and wiggle several times. Each time, the protein ends up a slightly different position, but you'll find that progress slows as you repeat the process.
You can also use the move tool to adjust the position of the design section. After moving the design section, you can again try mutating, shaking, and wiggling.
At the start, you may want to adjust the wiggle power. Starting with low wiggle power speeds up recipes like EDRW. Switching to medium wiggle power can help to refine the protein towards the end of the puzzle.
The large protein in this puzzle can be found the Protein Data Bank, as entry 1IJY. It's a mouse protein that's involved in how the animal develops. This protein also gets activated in many types of cancer. Binding to the protein might help fight these types of cancer.