The human body is made up of thousands of proteins. A protein is a long string of amino acids that, when stretched out, form a long "cord." The various amino acids along the cord are attracted to each other. This attraction causes the protein to bend around and connect with itself at these points of attraction. Since proteins are made up of hundreds of amino acids in various arrangements, the number of connections and the location of these connections vary widely. The process of a protein bending to form a complex structure is called folding.
The way proteins fold is key to understanding how proteins work in the body. Proteins are essential for human life because of the complex structures that they form. If a protein does not fold correctly, it could function as a toxin in the body. Understanding how proteins fold can give scientists insight into how to correct proteins that do not fold properly. Misfolded proteins are linked to numerous diseases, which could be cured once we have a better understanding of protein folding.
Scientists use super computers to predict the way proteins fold. However, computers are not good at figuring out the complex structures of proteins and must "brute force" the problem by simply trying all permutations of the possible ways a protein could fold. This is very expensive and requires a vast amount of computer time. Unlike computers, humans are extremely well adapted at finding the patterns within the protein molecules. Foldit plays to the human strength of pattern recognition by giving players a protein to solve. The game scores the player on how well they can fold the protein into a proper structure. Thousands of people collaborate on these various puzzles until a correct solution is found.
Already gamers have found numerous protein folding sequences that computers could never crack.
Foldit scores players on three key criteria:
Size of Protein
Proteins naturally form very compact structures. They are so tightly packed that not even a single water molecule can pass through them. Players much try to fold the protein in such a way that they avoid "voids" within the structure of the protein. The tighter the structure, the higher the score the player will receive.
Hydrophobic and Hydrophilic Atoms
Certain atoms and molecules are repelled by water and some are attracted to water. Naturally, the atoms that are hydrophobic (or scared of water) want to migrate as far away from the water that surrounds a protein in the human body. For this reason, players must try to "hide" all the hydrophobic atoms in the inner portion of the protein as they fold. Hydrophobic and hydrophilic (water loving) atoms are color coded: orange and blue, respectively. The player is scored on how well they can hide the hydrophobic atoms and how well they can expose the hydrophilic atoms.
Distance Between Atoms
Atoms generally do not like to be too close together unless they join in a bond. Players must make sure atoms have adequate spacing apart from each other throughout the structure of their protein to receive a high score. When two atoms are too close together, the game will signal a spiked red ball to indicate a clash. These clashes must be corrected before receiving a good score.
Foldit uses cell shaded style graphics with thick black outlines around objects. The graphics were made to look pleasing and keep gamers interested as well as make the various regions of the protein stand out. The game runs with hardware acceleration supported.
While the game itself is a single player affair, the creators of the game highly encourage collaboration with other players to solve the most complex proteins. Proteins can have hundreds or thousands of folds and connections, so players are encouraged to help each other with hints and tips as well as partial and full solutions. The Foldit community is rather large and continuing to grow.
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