Folding@Home 2.0 - An Online Protein Folding Game

a boy named woo writes "Tired of justifying your gaming addiction? Now you can really help accomplish something while you play... thanks to Howard Hughes Medical Institute researcher David Baker at the University of Washington." In collaboration with others, Baker has designed a game, called "Foldit," with a practical outcome: players manipulate on-screen images of protein chains and attempt to predict their folding patterns. From the article: "'Our main goal was to make sure that anyone could do it, even if they didn't know what biochemistry or protein folding was,' says [co-creator Zoran] Popovic. At the moment, the game only uses proteins whose three-dimensional structures have been solved by researchers. But, says Popovic, 'soon we'll be introducing puzzles for which we don't know the solution.'"

No Linux version and no source code

All that's there is the windows executable [fold.it] and the mac executable [fold.it].

Re:No Linux version and no source code

You mean it only supports >95% of computer users? What an outrage!

Re:No Linux version and no source code

I'm one of the game creators; and there IS a linux version, I use it every day, but somehow the story broke a day too early. Just hang on, please.

Re:

I just thought I'd warn you.... Jack Thompson is writing to your mum. He heard about an add-on that lets you shoot law-enforcement genes.

Is it that hard to actually link to the game?

http://fold.it/ [fold.it]

Re:Is it that hard to actually link to the game?

Thanks. Eds, take note: please use that link in tomorrow's dupe. kthxbye

Outsourcing bioinformatics!

From TFA:

"My dream is that a 12-year-old in Indonesia will turn out to be a prodigy, and build a cure for HIV,"

We should give David Baker credit for bringing forced child labor into the 21st century! Think about it: thousands of children, solving protein stuctures for 12 hours a day, 7 days a week, at $0.50/hour. The prescription drug companies could lay off all their bioinformaticians, outsource their drug discovery program to Indonesia, and cure cancer in one fell swoop.

Re:

Actually, this reminds me of a short-story(can't remember if it was Gibson or Sterling) about drug-company employees using VR gear to test molecule interactions: the protagonist enjoyed the simulation so much that she refused to take a promotion(and played

look mom, no more cancer

how about a quake mod?

Baker heads up Rosetta

Baker already heads up Rosetta@Home [bakerlab.org] , a BOINC [berkeley.edu] project that has your computer fold proteins in its spare time. He's appreciated for keeping his journal up-to-date and being responsive to participants; Folding@Home [stanford.edu] is somewhat less responsive (and doesn't provide the BOINC option).

Drugs get Copyrights ya?

From TFA: "Baker has high hopes that the game will speed up the sometimes tedious business of structure prediction. But the part of the game that excites him most is scheduled to debut this fall, when gamers will be able to design all-new proteins. Novel proteins could find use in any number of applications, from pharmaceuticals to industrial chemicals, to pollution clean up. With the ability for any person with a computer and an internet hookup to start building proteins, Baker thinks the pace of discovery could skyrocket. âoeMy dream is that a 12-year-old in Indonesia will turn out to be a prodigy, and build a cure for HIV,â he says." ...But will that 12 year old get to own the copyright and sell it to the drug company and make billions? Or will the drug companies just steal it and keep the money for themselves...

Re:Drugs get Copyrights ya?

Well if the company is smart they'd give him a job or scholarship or such. Anyway afaik drug companies never find proteins, they always "steal" them, i.e. patent the work of government paid university researchers, or buy the patents from the university for peanuts. All the drug companies actually do is the FDA "paperwork", which is actually quite costly, and the marketing.

In an ideal world, if the fed. gov. paid for the universities to do the research, they could also pay for the universities to get the drug some preliminary FDA approval. After that, any U.S. based (generic) drug company could produce the drug (completing their part of the approval process). However, only U.S. based companies would have this right.

Unprecedented

This is the first time I've seen a project that combined distributed computation, using human minds for intelligence and processing power, and connecting the two with an interface that is intended to be entertaining and pleasant. I'm eager to see if they get any good results. If this is successful, it may set a precedent for using large numbers of people to crunch the kind of problems that computers find prohibitively difficult.

Wait a sec...distributed computation, human minds, pleasant interface...starting to sound like teh Matrix.

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teh Matrix.

The marketing guys told us the matrix sounded scary and suspiciously close to something people heard in math class. It has been renamed the cloud - fluffy, pretty, sometimes looking like ducks or the virgin mary - for the public benifit.

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Part of the project actually is to determine what can make the game more fun. For me the funnest part is competing against others.

this could be the next big thing

I work in a protein engineering/structure lab that has strong connections to the Baker lab, both in people and in scientific collaboration. The biggest project to come out the Baker lab is a protein structural modeling, simulation and prediction suite known as ROSETTA. While I'll gloss over some of the nitty-gritty about the methodology, suffice it to say that ROSETTA, through a combination of knowledge based and physics based modeling, has knocked the pants off of just about every other program out there used to simulate, design, and fold proteins. (Quantum-based physics models can be much better than ROSETTA, at the expense of a few extra superclusters and months of simulation time).

I no longer work as a ROSETTA developer or the "protein folding problem", but many of my lab mates do. They struggle with ROSETTA sometimes, as it comes close to predicting the real structure of a protein, and then falls away and wanders into another structure far from reality. If only it could 'see' the best structure when it came close!

The problem can be analogized with surveying a landscape. Imagine every square feet of dirt you can see is one possible protein structure, and you want to find the lowest elevation square foot. For a human, the visual search process is fairly quick and rapid. You can see a few hills out in the distance, but a much lower valley on the other side, where the land is lowest. It takes only a few seconds. On the other hand,a computer with no prior knowledge of the landscape can take a very long time to find that global minimum. The computer essentially has to drop a ball on the landscape and watch where it rolls, then pick it up, put it somewhere else and watch again (Physics and computer modelers forgive me!). It may never pick the right starting point to get over that far away hill.

Perhaps the brain can be as good at finding great protein structures as we are at finding lowest elevation points. Perhaps intuition about how a protein 'should' look can get us places a computer program never can without a ton of time and power. That's what this game is all about. The baker lab has done a fantastic job of turning a very hard scientific problem into a competitive game that is simultaneously fun, provides possible scientific information, and represents something of a human experiment on how our brains work.

This could be the next leap forward if it turns out some people have an innate knack for folding. It should be interesting to watch.

OMG. This is INSIDEOUS. (I've just played it)

Sheer genius. I don't normally get into puzzle games but this one had me playing for 45 min straight before forcing myself to stop. It's well designed and fun to play.

With tetris it was time wasted down the tubes. At least with this you are doing something useful (and it might save somebody's life).

I can just see this thing going to cell phones, PDA's, etc.

Then there's johnny

Johnny discovered the cure for cancer when he was 13. He had the inspired notion to try to fold everything into the shape of a phallus. This, it seems, was the key all along.

National Geographic
March, 2012

>----Joke-----

I always figured protein folding was one of those "hard to do, easy to check" type of things. Then again IANAMB.

Re:----Joke-----

You are not a miniature boxer?

Re:----Joke-----

No, it's the other way around. There are many ways to fold it so folding is easy. But there is only one solution with the lowest (free) energy. The number of ways to fold is very large. To determine if your solution is the lowest, you have to check all possible ways of folding. So in this game, they'll let you fold and if you are better than all the human and computer opponents for a certain period, you probably get some points.

Re:

But letting people "game" certain types of folds permits these folds the ability to be removed from further calculation, right? You would be making progress either way. Personally, I think it would be cool if you could disguise the folding in other games

Well, the idea is to find out the solution

Well, another quote comes to mind: "I shall not today attempt further to define the kinds of material [under discussion] . . . but I know it when I see it." -- Supreme Court Associate Justice Potter Stewart, after failing to define what counts as obscene.

In this case, it's the program which knows it when it sees it. If the atoms can stay in that configuration, it's a solution. It's not known in advance, but it can be known if you reached a solution anyway.

On a more pragmatic note, though, well, the problem is that a human dragging atoms around is massively _slow_ compared to a computer. A puzzle you could realistically complete in a couple of days (i.e., before Joe Average completely loses interest, for lack of any visible progress or achievement or reward), the computer runs through them in seconds or minutes.

So basically simple proteins that you can realistically visualize and toy with as a puzzle, have been solved already anyway. Even if you managed to find a simple one that we don't already know how it folds, Folding@Home would run through it in seconds or minutes.

The problem are the big and complex ones. And I'd _really_ like to see anyone folding a beast like Hexokinase [wikipedia.org] by hand.

Or to give you an analogy, think of the game Atomino. Now think Atomino with several thousand atoms. It's not as much a puzzle, it's something straight from Call Of Chtulhu. If you even managed to wrap your mind around it all, well, it'll probably stay bent ;)

Re:Well, the idea is to find out the solution

Folding@Home on my PS3 take a couple hours at least per nanosecond of folding. A work unit is not a fold. It's a tiny fraction of a fold which can take thousands of nanoseconds. If a human can solve it in a day, that's a VAST improvement.

Re:Well, the idea is to find out the solution

The "game" has two options to automatically "shake and wiggle" a molecule for collisions and misalignments a computer can easily identify. You don't have to handle trivial collisions by hand.

But there are certain problems that are easy for a person because humans can visualize and imagine a structure, something a computer simply cannot. This is exactly what this program is about. You look at such a molecule and can easily determine that bending it here or there allows you to crunch it further. A computer would have to try all, or at least many, combinations that you already exclude as pointless just from looking at them.