Gamers Beat Algorithms At Finding Protein Structures

jamie writes "Researchers have turned the biochemical challenge of figuring out protein folding structures into a computer game. The best players can beat a computerized algorithm by rapidly recognizing problems that the computer can't fix. From the article: 'By tracing the actions of the best players, the authors were able to figure out how the humans' excellent pattern recognition abilities gave them an edge over the computer. For example, people were very good about detecting a hydrophobic amino acid when it stuck out from the protein's surface, instead of being buried internally, and they were willing to rearrange the structure's internals in order to tuck the offending amino acid back inside. Those sorts of extensive rearrangements were beyond Rosetta's abilities, since the energy changes involved in the transitions are so large.'"

In 10 years...

[velja27]

When humans have figured out how to connect their own brains in beowulf cluster, to harness the awesome power of the human mind, 30% of world population is going to be slave to corporations that need human brain power to do their bidding in order to do whatever that they do. But that's pretty much the same as it is now. But on the other side it really could be a nice job opportunity, go to work turn your brain on to some cluster be unconscious for 8 hours and go back home.

Congrats, you might already be a Nature co-author!

[damn_registrars]

If you go to the page for the Nature article [nature.com] that this Ars Technica article is based on, you can see the author list for the Nature paper:

Seth Cooper, Firas Khatib, Adrien Treuille, Janos Barbero, Jeehyung Lee, Michael Beenen, Andrew Leaver-Fay, David Baker, Zoran Popovi & Foldit players

So if you've played Foldit you have helped with the authorship of this paper. Not only that, but since it is a biological paper, you are a corresponding author (by virtue of being the last name on the list).

I would highly recommend listing that on your CV, or at least in your application to the Nobel Committee.

Re:I've played a bit

[the gnat]

forget about Foldit! Just download Folding@Home and let your CPU/GPU do it for you!

FoldIt and Folding@Home are doing completely different things. FoldIt (or more specifically, the Rosetta software underneath it) is attempting to guess the final structure of novel protein sequences, using a variety of clever tricks such as mining the database of known structures for peptide motifs. It contains energy functions to evaluate candidate structures, but it is not simulating physical processes, and it tells you nothing about how the linear chain of amino acids forms the 3D structure. Folding@Home is used to study the process of protein folding, where the end result is already known; it isn't useful as a structure prediction tool. Both programs require a massive amount of computing power, but for very different reasons. Both are very useful, but there is almost no overlap in their practical applications. (And it should go without saying that while they can both be an excellent complement to experimental studies, neither can replace them.)

Re:Bio chemistry question

[neo-phoenix243]

Essentially, catalysts can help proteins fold- such as other proteins helping a polypeptide strand be arranged into a particular structure.

Re:Bio chemistry question

[Methinx]

Two clarifications (rather than answers): Evidently, you mean chaperones that act by creating a confinement region (a cage) of boundaries (walls build of amino acids) of desired hydrophobicity distribution, where proteins of with improper conformations can get better. Protein atoms perform thermal movements so to a little degree they can search for an optimal conformation, but it's not enough - it seems that proteins are (sub)optimal by design (i.e. by evolution). I wrote sub~, because the global minimum POV is a hypothesis (and there may exist separated kinetic xor thermodynamic minima).

Re:Congrats, you might already be a Nature co-auth

[Zerth]

If the Andrew Leaver-Fay in this paper is the same one who cowrote "Faster placement of hydrogens in protein structures by dynamic programming" with Jack Scott Snoeyink, then yes. It gives a 4.

Best shot since I missed out on getting a 2 on Ebay.

Re:Great idea but seems tough to gamify problems

[fraktalek]

Foldit had the great insight to take you to an algorithmically close starting place and let you complete the final adjustments - in that way the algorithm itself is as much a part of the team as the detail or adjustment members they were talking about.

This kind of problem solving was suggested already by Stanislaw Lem in his book Summa Technologiae [wikipedia.org] as a kind of "augmented intelligence" as opposed to purely human or purely artifical intelligence.