A Framework for Scientific Discovery through Video Games. Seth Cooper

a bright, cartoonish look. Many pieces of the visualizations move playfully around the protein. There are a wide variety of visualization options available in the game as well, such as alternative colorings and geometries for the protein. These can be accessed through a special menu option that is turned off by default. This approach allows more advanced players the ability to customize their view in the view options menu, but keeps things simple for newcomers.

      Visualizations such as voids and exposed hydrophobics can be computationally expensive to compute. To keep the game interactive, we compute such visualizations in a separate thread, which will update the visualization after a delay.

3.4.2 Interactions

      Foldit also provides several different methods of acting on the protein. Figure 3.6 is a screenshot of user interaction. Players need actions that allow them to manipulate the proteins in a way which will bring them closer to their goal. They should be intuitive and useful; we have tried to structure our input around the idea of touchability, or direct manipulation. Whenever possible, we have tried to make operations act directly on the protein itself. Some of the possible actions the user can perform are:

      Pulling. This is intended to be the primary method of interaction. When the user clicks and drags on part of the protein, a purple arrow extends from the protein to the location of the user’s mouse cursor. The protein will then try to move to stay under the mouse, while still satisfying some energetic preferences.

      Bands. Purple bands can be placed by the user to attach one residue to another, or a residue to a point in space. When the user performs another operation on the protein, bands will pull on the attached residues. This can allow the user to keep parts of the protein in place, pull to specific points in space, or pull in multiple places at once.

      Figure 3.6 Foldit’s main game screen during interaction. The puzzle Collagen is shown. The player is acting on the protein. The icy blue sheet is locked and the purple cylinder with the round end is a band. The purple cylinder with the pointed end shows where the user is pulling on the backbone. The dark blue part of the backbone is affected by the pull.

      Locks. Locks prevent the protein from being affected by operations. The user can lock individual residues or whole secondary structures, giving them an ice-like appearance. Locks allow a kind of implicit selection; by locking two residues, the user can then easily operate on the residues between them.

      Wiggle and shake. Wiggle and shake are two automatic actions the user can launch. Wiggle performs an optimization over the backbone, and shake performs an optimization over the sidechains. They can be performed globally as well as locally by using locks.

      Rebuild. Rebuild allows the user to specify a section of the protein to be modified primarily by Rosetta fragment insertion, a process of copying backbone angles from similar native structures. This operation has a large element of randomness and can result in drastic changes to the structure.

      The interactions in a scientific discovery game must also meet several criteria. They must respect the constraints of the system required. However, they must also be sufficient to explore the space of solutions enough to be able to solve the problem. They should also be as intuitive and fun as possible.