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Some words from the Foldit blog.

Foldit is a hard game. There's sometimes scientific terminology involved, which doesn't makes things easier. Knowing just a little bit of the jargon can make the game a lot easier to understand. Here are twenty important words in Foldit, and a brief explanation of what they mean. Check out the glossary for more.

  1. Protein - Foldit is all about folding and proteins. We've had at least one RNA puzzle, and there are a couple of Intro Puzzles that include DNA. Small molecules called ligands show up in some puzzle. In Foldit, "the protein" can be any of these things in general.
  2. Segment - proteins are chains of Amino Acids, and each link of the chain gets a segment number. Ligands, RNA, and DNA have segment numbers. Segments of a protein are often called residues just to keep everyone confused.
  3. Sidechain - each amino acid has a different sidechain. You can often tell which amino acid is which by just the shape of the sidechain. The Amino Acid Gallery has pretty pictures.
  4. Backbone - the backbone part of each segment is chemically the same, but it can have many different shapes. RNA and DNA, have backbone too, but different chemistry for each.
  5. Helix - sometimes the backbone forms a spiral or helix. Hydrogen bonds along the helix backbone make it strong and springy.
  6. Sheet - you may see zigzag lightning bolt shapes along the backbone. These flat sections are called sheets. Hydrogen bonds form between the edges of the sheets (also known as strands), helping stabilize the protein.
  7. Loop - helix and sheet are the major types of secondary structure. Segments which don't have these shapes are called loop.
  8. Shake - shake moves the sidechains around, trying to find a better position for them. It leaves the backbone unchanged.
  9. Wiggle - wiggle tries to fine-tune the position of the backbone and the sidechains. Wiggle often causes parts of the protein to move around as the backbone changes shape.
  10. Clashes - clashes are shown by spiky red balls, and happen when two atoms get too close to each other. Their electrons just can't get along. You can adjust Clashing Importance to smooth things over temporarily.
  11. Hiding - some amino acids are hydrophobic, meaning they are repelled by the (invisible) water that's all around the protein. You want to hide hydrophobics in the core of the protein, away from water as much as possible. Hydrophobics near the surface are called exposeds, and may be highlighted by blotchy yellow balls.
  12. Packing - clashes are bad, but proteins shouldn't contain too much empty space. Voids occur when a protein isn't packed tightly enough. Voids show up as translucent red blobs.
  13. Ideal - you'll see references to "ideal" shapes and angles. "Ideal" actually has two different but related meanings in Foldit. In the original sense, "ideal" meant perfect based on calculations, but it's expanded to include values determined by examining many real proteins.
  14. Band - you can always pull on parts of the protein to change the shape, but bands offer finer control. You can adjust the length of a band to determine whether it pulls or pushes. You can band from the protein to itself, or to a point in space.
  15. Cutpoint - in Foldit, you can't break the strong peptide bonds that hold a protein together, but you can use temporary cutpoints, which let you move parts of the protein separately. You must close open cutpoints for your score to count.
  16. Recipes - a recipe is a small script or macro that does something to the protein. Most recipes are written the Lua scripting language. Recipes are good for slow or repetitive tasks. Recipes live the cookbook.
  17. Rebuild - rebuild picks different shapes for a part of the protein. Many recipes do rebuilds, and finding a good one can take a long time.
  18. Remix - remix is similar to rebuild, but has a different strategy for picking shapes. Remix has a much better user interface than rebuild, so it's actually possible to remix by hand. Finding a good remix can still be slow, so recipes still get invovled.
  19. Fuse - fuse is a strategy for improving the protein by shaking at wiggling with different levels of clashing importance set. You can fuse by hand, but many recipes do fusing as well, either by itself, or as part of other changes, such as rebuilding or remixing.
  20. Design - Foldit has been offering design puzzles since its earliest days. Some design puzzles have specific target, while others allow players to design a protein completely from scratch. Players have been successful in designing proteins which fold up on their own, see Design puzzle results for the latest.
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