What do you do with an unpredictable protein structure?

You Foldit! Foldit, as in the science-based puzzle game. In my last post, I already talked a little bit about this phenomenal game. I decided to look into it with a more in-depth perspective. I found a scientific journal entry and dared to share my findings. Unfortunately, I must confess that I'm not well-informed with science term lingo, but the main points I want to make about Foldit are still intact.

First, let's recap on what this thing is. In the journal's words it describes Foldit as "a multiplayer online game that enlists players worldwide to solve difficult protein-structure prediction problems" (pg.1). Players have to use all sorts of things like three-dimensional problem solving skills to the use of teammate skills, but thankfully an understanding in molecular biology is not required. The game gives high scores, which depend on the low energy of the protein, and has different tools that allow players to create and predict protein models.

The journal talks about how there are many protein modeling problems that are cooperative to comparative modeling from the structures of homologous or similar proteins. The journal also says that, "To make use of homology modeling techniques in Foldit, we introduced a new capability called the Alignment Tool, which allows players to manually move alignments and thread their sequence onto the structures of known homologs" (pg.1). So, a similar protein is given and it is the players'jobs to find a new protein by making very tiny tweaks here and there, a term referred to by the journal as "tunneling".

The creators of Foldit held a competition in order "to determine whether human intuition could succeed where automated methods had failed, [they] challenged Foldit players to build accurate models of M-PMV PR" (pg.3). The M-PMV PR is an AIDS causing monkey virus. For over a decade, even with several crystallized forms, researchers have been unable to solve the protein structure using several different methods, one of them being model replacement. After only three weeks, when the competition ended, the researchers looked at the top-scorers' models. Several solutions were actually good enough estimates that it allowed a rapid solution for the crystal structure. As the players progressed for a few days, they finally completed a final superior, polished structure.

The last paragraph in the journal sums up the purpose of Foldit ,which goes hand in hand with the blog. It shows the power of online games and how it uses human intuition and three-dimensional pattern-matching skills in order to find a solution to difficult scientific problems. Much attention has been given to game playing potential, but for serious scientific problems this may be the first example of how online gamers can help. Page three, the last page,  gives the final conclusion of the actual potential, "These results indicate the potential for integrating video games into the real-world scientific process: the ingenuity of game players is a formidable force that, if properly directed, can be used to solve a wide range of scientific problems."
Are you excited to know how games can be used for medical and scientific purposes, or do you think this will all blow over and Foldit was simply a unique but not very repeatable idea?
Let's keep playing!


Khatib, F., DeMaio, F., Cooper, S., Kazmireczyk, M., Gilski, M., Kryzwda, S., Zabranska, H.,Thompson, J., Popovic, Z., Jaskolski, M., Pichova, I., & Baker, D. (2011). Crystal structure of a monomeric retroviral protease solved by protein folding game players. Nature Structural and Molecular Biology, 3. Retrieved from http://www.nature.com/nsmb/