Foldit

Foldit is an experimental computer game designed to help scientists in the optimization of proteins. It is developed in collaboration with the departments "Computer Science and Engineering " and " Biochemistry " at the University of Washington; among other things, many people of the Rosetta @ home project are involved. The approach of Foldit is a combination of crowdsourcing and distributed computing. The first public beta version was released in May 2008.

Design and purpose of the game

The aim of the game is to get a best possible " folded " protein, ie a model of the protein in a state of minimum energy. This is the form in which it occurs in nature. This, however, no previous knowledge is required, the assessment done by the program. The possibilities that the player has to protein engineering are explained in a series of tutorial puzzles. For the game a graphical representation of the protein structure is displayed, which can change with different tools of the players.

If the structure is altered, the program calculates a score based on how well the protein is folded. For each puzzle, a high score is calculated for both individual as well as group solutions, the changes in real time.

The process of synthesizing the living being, the primary structure of a protein, the protein is fairly well understood, as well as the encoding DNA. To determine how the primary structure of a protein is transformed into a functioning, three-dimensional structure - how the protein folds - is more difficult. The general process is known, but the protein structure prediction requires a lot of computation time, rising sharply with increasing length of the protein, and is imperfect.

Foldit is an attempt to put the natural human 3-D pattern recognition skills to this problem. Current puzzles are based on well-understood proteins. By examining the way in which to approach the player intuitively to these puzzles, the scientists try to improve existing protein folding software. 2008 took part in the Foldit protein prediction competition CASP8 and cut despite little experience of the players and some half-baked tools very well. In half of the cases achieved a top 3 placement and once the top spot ( 71 to 83 participating laboratories, two times 527). In each case, all the models were calculated only from computers were exceeded.

Achievements

M -PMV protease

In September 2011 ( Mason - Pfizer monkey virus retroviral protease ) was Foldit of the structure of the monomeric protein M -PMV protease decrypted the causes AIDS in rhesus monkeys.

Diels- Alderase

In January 2012 it was announced that Foldit players managed the redesign of a protein with a 18 -fold higher activity than the original. The protein is a computer- created enzyme that catalyzes the Diels- Alder reaction. The Foldit players revised the enzyme by the addition of 13 amino acids and thus increased its activity by 18-fold.