The Basic FoldIt Controls and the Way Nature Folds Protiens

When playing FoldIt you have some controls you use all the time and some you use less frequently.  The Actions you use all the time are Shake Side chains, Wiggle  All, Wiggle Backbone, Wiggle Side chains, Unfreeze Protein, Remove Bands, Disable Bands, and (unshown) Enable Bands.  In addition to these Actions, I have demonstrated a frozen segment and a band between a segment and space.  You can also band and freeze side chains.  I have also brought up the local action popup menu where you can Freeze or Tweak the structure(if the segment is part of a helix or sheet) or Rebuild, Shake, or Wiggle the protein as bounded by frozen segments.  The Behavior menu item brings up a slider for Clashing Importance.  Some puzzles let you Mutate Side chains.  Some puzzles have ghost guides of the native protein fold.  Some puzzles allow the protein to be threaded by aligning it against other proteins with known folds.  The Modes are Pull, Structure, Note, and Design.  I play most of the game in Pull mode.  Structure mode lets you indicate a segment as being part of a loop, helix, or sheet.  Note mode lets you add comments to segments so you can document what you want to do and where.  When a Puzzle lets you mutate the protein Design mode lets you change the amino acid at a particular segment and to insert or delete segments in puzzles that let you change the number of segments.

Since the idea of the game is to help science these control need to be analogs of natural processes.  When you Google Protein Shape you find some interesting articles about why protein take the shapes they do.   When I ran the query the first page returned was to The Rules of Protein Structure by J Kimble, the second was to The importance of protein folding by Joachim Pietzch.  Later I found How Proteins Get In Shape, an unattributed article on the Pittsburgh Supercomputing Center Website.  A scan of the cited articles and others you find from the search should give you an idea about the shake and wiggle actions and even the clashing importance.  The freeze and band controls are a bit more mysterious.  For the most part the take on the role of all the natural processes too complex to individually model with today's technology.

You can help science by more than just playing the game.  You can record the techniques you use in "Recipes" and share them with others.  In a previous article I touched on recipes.  I will return to them in my next article.