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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.'"
Yay, everyone's a winner!
I always figured protein folding was one of those "hard to do, easy to check" type of things. Then again IANAMB.
(rot13) rpbzbab@tznvy.pbz
All that's there is the windows executable and the mac executable.
DNA is the ultimate spaghetti code.
http://fold.it/
Technoli
You are not a miniature boxer?
Who's to say that the wrong sort of mind will try to use this to make biological weapons of some sort? If it can be used to create beneficial wonders, it can be used to create terrible horrors.
Captain's log, stardate 41358.2. I am nailed to the hull.
Comment removed based on user account deletion
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.
DNA is the ultimate spaghetti code.
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.
- Demosthenes
cynicsreport.com
Could be the next test of the true talent of a programmer. These have to be the most complex 3D problems ever. If a person were good at it , would probably be a paying occupation.
I'm a PhD student doing molecular structural biology (aka solving structures by 'real' experiments), I do wonder when these programs will start becoming accurate enough or even better to get novel structures compared to doing the classic crystallization / X-Ray experiment or NMR.
And if they become accurate enough does this mean that people will (have to) do the classic experiments to confirm the structure prediction?
No, he's not a mama's boy.
I prefer rogues to imbeciles because they sometimes take a rest.
how about a quake mod?
Words to men, as air to birds.
Seems like the editors aren't doing their job. http://fold.it/
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 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
A polar bear is a cartesian bear after a coordinate transform.
Baker already heads up Rosetta@Home , a BOINC 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 is somewhat less responsive (and doesn't provide the BOINC option).
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...
If you look at known sequence patterns (motifs) then you can assume it will fold the same, try to fit it and compare the fold with other proteins with the same motifs whose structures have been solved experimentally.
Protein folding is a very interesting subject that has seen some big advances over the years but we're still at the very beginning.
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.
I'm a little wary. I remember the first and only time I used the Folding@Home client a few years ago on Windows 2000. A few hours into using it my computer blue-screened. The usual chkdsk stuff didn't work; the system got so throughly corrupted I had to re-install Windows. I know Folding has an admirable goal and it might of just been a fluke, but I don't think I'll ever install their software again.
http://www.mininova.org/tor/1392891
Not usable for me.
The adenosine triphosphate is a lie!
A better game that is sort of similar involves folding eggs around cars, and the protein damages the paint!
Orbis terrarum est non altus satis
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 like FPS where shooting certain bots triggers a fold of a certain kind on you, the protein molecule. Make the calculation minute and let some gamer perform it as many times as they want checking to see if it works or not.
Every time I start to have faith in humanity, I ruin it by driving to work between 7 and 8 am.
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.
-Ryan
AUWYHSTOT (Acronyms are Useless When You Have to Spell Them Out Too)
This game is an offshoot of the rosetta@home effort to model protein folding. Folding@home is a separate effort.
Yeah, I've been playing it.. it's pretty awesome. I have no idea what I'm doing but my score goes up.
As such, I'm pretty sure genetic algorithms could give similar performance.
How we know is more important than what we know.
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.
Your argument is true about nearly every piece of science and technology ever created.
No, you don't get some points.
You get to stand between their clothes dryer and laundry basket for the next game, and show off your '1337' folding skills.
*ducks and runs- 'cause I Am Not A Miniature Boxer either*
Down With Slashdot BETA!!! I've been around the corner and seen the oliphant; you can only abuse me from your perspecti
I like the Facebook Genetics Application
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
today is spelling optional day.
In this project users will map variables onto ingredients of typical recipes. After combining and cooking, the flavor of the resulting dish will determine which equations can be solved.
You got to know how to hold em, know when to fold em,
Know your alpha helix and beta sheets.
You never count your units when you're sittin' at the keyboard,
There'll be time enough for countin' when the protein's done.
Laissez lire, et laissez danser; ces deux amusements ne feront jamais de mal au monde. - Voltaire
Seriously: I know that's a bit subjective, but I (and literally millions of others) disagree with that. I run BOINC on my computers because it does *not* suck. I run several projects on each, ensuring that when/if one has a server outage or workunit lull, my BOINC clients are doing something useful for someone *else*.
Perhaps you've never heard of or used the account managers BAM or GridRepublic; they make managing projects and client computers a breeze. They're easy to use but quite flexible.
I wholeheartedly think their functionality should have been built into BOINC from the get-go, but perhaps the authors of BOINC (the Berkeley team that does seti@home) omitted it intentionally because *someone* has to run the software and they didn't want to be the ones.
Folding@home is a big and well-funded project that doesn't benefit from the middleware that is BOINC, but they also reap no benefits from the network effect that such a wide userbase offers.
So no, I don't think BOINC sucks anything like "really really bad". If you're happy with Folding@home, fine; but don't slander BOINC and thus the dozens of projects that use it simply to re-enforce your own decision, especially in such a shallow way. (TWO "really"s with a "suck", and no other commentary? This guy must be both serious and knowledgeable.) BOINC ain't perfect, but it's pretty good already, and continues to improve over time.
They should port this to the wii, Cant you just imagine it? 4 players competing to fold proteins
(Physics and computer modelers forgive me!) (Ouch.) You're describing gradient descent, which requires a coherent solution space and a differentiable heuristic for "descending" through it to the most optimal solution subject to the constraints of the function being investigated. 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 So your search algorithm uses a probabilistic, shotgun/Battleship!-style approach to carpet-bomb the solution space, or perhaps (guided by some heuristic) just the "interesting" parts of it? I suppose this is niggling, but is there some reason not to use a momentum factor, or try several, since that's job-level parallelism (which you have with BOINC)? It may never pick the right starting point to get over that far away hill. With a momentum factor, it needn't. The price paid is a loss of precision in the descent algorithm, which might miss an optimal solution if that solution were only slightly more optimal than nearby solutions. To further abuse your analogy, the ball might roll right over the lowest point if it either didn't fit or is going so fast when it gets there that it rolls right up into local minimum with steeper inside slope. Perhaps intuition about how a protein 'should' look can get us places a computer program never can without a ton of time and power. I'm quite skeptical. This is GalaxyZoo, except you have to make your own galaxies based on intuition about how they "should" look (and constrained to the relevant laws by the software). I haven't tried it out or read any papers (any extant?) on this, but it seems like a shot in the dark. It's a small investment by the humans, but if they guess right then this could solve an incredibly hard problem and pay off big-time.
Adenosine triphosphate is people!
"Currently, the username is rp and the database server is db1."
Is it that usual to give username and password of database over the net ?
C. Sagan : A demon haunted world:
http://www.amazon.com/gp/product/0345409469/
visit randi.org
I'm holding out for FoldingFolding@Home Revolution.
Shop as usual. And avoid panic buying.
http://uwnews.org/article.asp?articleID=41558
But I couldn't get it to fold my clothes. Damn!
This software has appeared, interestingly enough, the same week as the biannual Critical Assessment of Structure Prediction competition has started.
:)
I wonder if there is some connection...
I've not looked at the software yet but if I start seeing PDZ domains then I think my suspicions will be confirmed.
Humans can imagine and visualize _simple_ structures, yes. More complex stuff, well, I posted a link to a picture of Hexokinase. You try visualising and imagining that. If you can, well, you have a better imagination than I do
A polar bear is a cartesian bear after a coordinate transform.
As others have said: this is fascinating. It makes sense too: Games are practical problem solving wrapped in eye candy and sometimes a story. Why not solve a useful problem why you are at it? The distributed wetware aspect is very cool as well.
I wonder: did you consider implementing the client in java? Will we see this game on cell phones or PDAs?
___
No power in the 'verse can stop me
It froze on the loading of game 4 for me. Sucked up 100% of the CPU and wouldn't respond. Seemed slow before that point too. Might be an OK puzzle game but only if they get it working.
I think this is really neat -- using humans to pattern match and solve puzzles rather throwing a brute force algorithm at $100 million in hardware.
It just makes good business sense. They could outshore this to India and save pennies on the dollar!
So don't take my phone calls, cure my AIDS! I'm not just sure this will work, I'm "HIV positive"!
nor a massive bitch
You can use Linux Folding@Home, you just have to buy a PS3. That counts, right?