Level 8-2 Ligand Constraints

Ligand Constraints. Use the move tool to move the ligand toward the protein. Then use the Wiggle Sidechains tool followed by the Shake tool.

In this puzzle, the Wiggle Sidechains tool is available. In regular Foldit puzzles, there are three versions of wiggle: wiggle sidechains, wiggle backbone, and wiggle both backbone and sidechains. The "wiggle both" version is the one more commonly used, but the other versions come in handy at times.

In this puzzle, there's again a small ligand, and a much larger protein. Red constraints will tend to pull the ligand toward the protein during a wiggle.

To start, click on the ligand to open the move tool. The right-click and drag (or control-click and drag) on the purple arrow to move the ligand closer to the protein, making the constraint lines shorter.

Next, use the Wiggle Sidechains tool (or keyboard shortcut "E") to wiggle the ligand and the sidechains of the protein. Let the wiggle sidechains run for a bit, then use Shake if needed to finish the puzzle.

You can also try skipping the move tool, and use Wiggle Sidechains followed by Shake. Since constraints act much like bands, the Wiggle Sidechains pulls the ligand toward the protein.

Madde's "Ligand Constraints" video

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