Beta
×

Welcome to the Slashdot Beta site -- learn more here. Use the link in the footer or click here to return to the Classic version of Slashdot.

Thank you!

Before you choose to head back to the Classic look of the site, we'd appreciate it if you share your thoughts on the Beta; your feedback is what drives our ongoing development.

Beta is different and we value you taking the time to try it out. Please take a look at the changes we've made in Beta and  learn more about it. Thanks for reading, and for making the site better!

Folding@Home 2.0 - An Online Protein Folding Game

timothy posted more than 6 years ago | from the folding-@-play dept.

Biotech 129

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.'"

cancel ×

129 comments

Sorry! There are no comments related to the filter you selected.

A Simpsons quote comes to mind (1, Funny)

Anonymous Coward | more than 6 years ago | (#23343568)

But, says Popovic, 'soon we'll be introducing puzzles for which we don't know the solution.'"

Yay, everyone's a winner!

>----Joke----- (2, Funny)

Eco-Mono (978899) | more than 6 years ago | (#23343604)

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

Re:----Joke----- (5, Funny)

Anonymous Coward | more than 6 years ago | (#23343618)

You are not a miniature boxer?

Re:----Joke----- (0)

Anonymous Coward | more than 6 years ago | (#23343700)

No, he's not a mama's boy.

Re:----Joke----- (4, Insightful)

oever (233119) | more than 6 years ago | (#23343658)

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:----Joke----- (2, Informative)

Anonymous Coward | more than 6 years ago | (#23343794)

But there is only one solution with the lowest (free) energy.
But therein lies the crux of it - not all biological molecules follow the lowest (free) energy model. They may have been forced into a specific fold by other proteins or stabilized by other means. Just assuming lowest (free) energy fold = right fold is not correct and unfortunately the only metric available for completely unknown folds.
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.

Re:----Joke----- (2, Interesting)

nschubach (922175) | more than 6 years ago | (#23344048)

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.

Re:----Joke----- (1)

rts008 (812749) | more than 6 years ago | (#23344780)

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*

Well, the idea is to find out the solution (4, Interesting)

Moraelin (679338) | more than 6 years ago | (#23343734)

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 (4, Insightful)

mweather (1089505) | more than 6 years ago | (#23344056)

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 (1, Flamebait)

blair1q (305137) | more than 6 years ago | (#23344552)

Your PS3 has a tiny fraction of the computing power of a current quad CPU and triple-SLI gaming cards. Throw in a dedicate physics-engine chip, and a decent gross-solution partitioning algorithm, and there's little that the computer can't do faster than you.

It's silly of these "researchers" not to put some real brainpower on that.

Re:Well, the idea is to find out the solution (2, Interesting)

LinuxGeek (6139) | more than 6 years ago | (#23345030)

Not quite right [stanford.edu] . There is a big difference between PPD and actual work produced, scoring varies for cpu, ps3 and gpu results.

Re:Well, the idea is to find out the solution (1, Insightful)

Anonymous Coward | more than 6 years ago | (#23345378)

Have you tried playing the game? You're pulling atoms around, but you also have the same toolbox that the computer has when it's trying to fold a protein, including gradient-based minimization, side-chain repacking, and cavity detection. The idea behind fold.it seems to be that humans might have better judgement about how to applies the tools used for protein structure prediction.

Also, Folding@Home takes an extremely long time to fold proteins of any reasonable size compared to a program like Fold.It. The submission title is a misnomer: Folding@Home is totally unrelated to Fold.It, they're totally independent pieces of software that represent very different approaches to molecular simulation.

Re:Well, the idea is to find out the solution (4, Insightful)

Opportunist (166417) | more than 6 years ago | (#23345492)

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.

Re:Well, the idea is to find out the solution (1, Funny)

Anonymous Coward | more than 6 years ago | (#23346090)

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 ;)

OK, that's it. I'm signing up now!

(Dude, seriously, if you're not on the project staff, you should be -- on Slashdot, that sort of comment is the best recruitment invite that could possibly be written.)

No Linux version and no source code (4, Informative)

oever (233119) | more than 6 years ago | (#23343612)

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

Re:No Linux version and no source code (5, Funny)

Anonymous Coward | more than 6 years ago | (#23343836)

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

Re:No Linux version and no source code (-1, Troll)

Anonymous Coward | more than 6 years ago | (#23344068)

Oh noes! No Source Code!11!!

Re:No Linux version and no source code (1)

mweather (1089505) | more than 6 years ago | (#23344070)

Or approximately 1% of the people geeky enough to try this.

Re:No Linux version and no source code (2, Funny)

Danathar (267989) | more than 6 years ago | (#23344606)

Have you tried it? It's INCREDIBLY addicting and just about as simple as Tetris to play. My mother picked it up in under 5 min and was playing for HOURS.

That's enough for me. It's going to be hit.

Re:No Linux version and no source code (5, Interesting)

laddiebuck (868690) | more than 6 years ago | (#23344096)

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:No Linux version and no source code (3, Funny)

Anonymous Coward | more than 6 years ago | (#23344386)

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.

Re:No Linux version and no source code (2, Insightful)

1 a bee (817783) | more than 6 years ago | (#23344618)

Do post back here, then, when the Linux version is ready, please...

Re:No Linux version and no source code (1)

t35t0r (751958) | more than 6 years ago | (#23345846)

is there way to change the settings so that I can go to the last level in offline play? Is there a registry setting?

Re:No Linux version and no source code (1)

t35t0r (751958) | more than 6 years ago | (#23345996)

figured it out just change "complete" to "1" in the .ir_puzzle files.

Re:No Linux version and no source code (1)

t35t0r (751958) | more than 6 years ago | (#23346146)

is there a way to convert the solution files to pdb files?

Re:No Linux version and no source code (1, Insightful)

Anonymous Coward | more than 6 years ago | (#23344184)

All that's there is the windows executable
And it required administrator privileges to install. Will anyone every learn to problem properly for Windows?

Re:No Linux version and no source code (3, Funny)

ORBAT (1050226) | more than 6 years ago | (#23345372)

And it required administrator privileges to install. Will anyone every learn to problem properly for Windows?
Now that's a Freudian slip if I ever saw one.

Re:No Linux version and no source code (2, Informative)

belmolis (702863) | more than 6 years ago | (#23344868)

Just in case you're tempted, I tried it under Wine. The installer ran fine, but the game itself doesn't work.

Re:No Linux version and no source code (0)

Anonymous Coward | more than 6 years ago | (#23345326)

I tried it under wine .9.6, and playing offline worked.

Re:No Linux version and no source code (1)

t35t0r (751958) | more than 6 years ago | (#23345686)

It installs and plays fine under wine-0.9.60. I couldn't login because it said my account was still pending. My mom who is a crystallographer and builds proteins using more sophisticated versions of these programs played it for a few minutes and got really into it. The score is most probably based on a phi-psi torsion angle plot called a Ramachandran plot as well as other properties (e.g. hydrogen bonding, close contacts, hydrophobicity, etc). This is really ingenious.

Re:No Linux version and no source code (1)

belmolis (702863) | more than 6 years ago | (#23346070)

Interesting. My wine is 0.9.30. I guess 3d-level release numbers for wine are not just bugfixes.

Is it that hard to actually link to the game? (4, Informative)

Conspiracy_Of_Doves (236787) | more than 6 years ago | (#23343616)

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

Re:Is it that hard to actually link to the game? (2, Funny)

Profane MuthaFucka (574406) | more than 6 years ago | (#23344840)

Oh darn you, you gave away the answer to the puzzle of the missing link. And I was SO CLOSE to solving it myself.

Re:Is it that hard to actually link to the game? (1)

p3d0 (42270) | more than 6 years ago | (#23345608)

"Darn you"? Not exactly living up to your name there.

Re:Is it that hard to actually link to the game? (0, Offtopic)

Profane MuthaFucka (574406) | more than 6 years ago | (#23346108)

Current mode = karma whoring. My other mode is fucking pudge in the ass. Oh, and also trying to get operagost to help me bone operagost's wife. So far he refuses to help.

Re:Is it that hard to actually link to the game? (4, Funny)

sootman (158191) | more than 6 years ago | (#23345484)

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

Then again (2, Interesting)

TheShadow1276 (1123869) | more than 6 years ago | (#23343630)

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.

Re:Then again (0)

Anonymous Coward | more than 6 years ago | (#23343752)

Oh brother... :) the americans.

Re:Then again (1)

Gat0r30y (957941) | more than 6 years ago | (#23343808)

Um, how precisely are you planning on folding proteins into evil ways? All you get here is a game where you fold em, your not doing much anything else. Puree of FUD.

Re:Then again (1)

mweather (1089505) | more than 6 years ago | (#23344110)

Um, how precisely are you planning on folding proteins into evil ways?
Fold them into prions, then load them into artillery shells. 100% fatal, and no cure.

Re:Then again (1, Insightful)

Anonymous Coward | more than 6 years ago | (#23345266)

+1 Funny? Or just another fucking idiot? It's so hard to tell these days...

Re:Then again (1)

chartreuse (16508) | more than 6 years ago | (#23346220)

Maybe brilliant. Something that refolded lots of proteins in your body would probably be lethal.

That's true about everything (1)

bigtrike (904535) | more than 6 years ago | (#23344702)

Your argument is true about nearly every piece of science and technology ever created.

Quote cut short. (1)

conner_bw (120497) | more than 6 years ago | (#23343634)

"... furthermore, we will also be introducing our laundry into the game truly harnessing the power of internet!"

Outsourcing bioinformatics! (5, Funny)

cynicsreport (1125235) | more than 6 years ago | (#23343660)

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.

Sorry; oblig. Re:Outsourcing bioinformatics! (2, Funny)

NotBornYesterday (1093817) | more than 6 years ago | (#23343710)

thousands of children, solving protein stuctures for 12 hours a day, 7 days a week, at $0.50/hour
A Beowulf cluster of them?

Re:Outsourcing bioinformatics! (1)

strider2k (945409) | more than 6 years ago | (#23343798)

I can't even imagine a 12 year old working on that. Sure there are prodigies in math and science but protein folding is out of the chart. Education provided to a 12 year old usually does not include Advance Cellular Biology or Molecular Biology.

Re:Outsourcing bioinformatics! (1)

zolf13 (941799) | more than 6 years ago | (#23343832)

... tempting idea ... now we know why they give away those XOs for free.

Re:Outsourcing bioinformatics! (3, Interesting)

Scott Francis[Mecham (336) | more than 6 years ago | (#23344392)

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 dumb on aptitude tests) so that she could keep "playing the game".

Re:Outsourcing bioinformatics! (1)

rossdee (243626) | more than 6 years ago | (#23344812)


Yougsters these days have it too easy, we used to have to work 29 hours a day, and pay mill owner for permission to come to work...

Re:Outsourcing bioinformatics! (1)

DecoyMG (228535) | more than 6 years ago | (#23344878)

Actually they are planning to give the program to middle school students, have to satisfy NSF's outreach activity requirements after all.

Re:Outsourcing bioinformatics! (1)

Provocateur (133110) | more than 6 years ago | (#23345796)

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.

Damn, I could probably have my very own vat-grown ninja, thaw when needed, to get those kids off my lawn! After they've migrated here, of course.

Re:Outsourcing bioinformatics! (1)

chartreuse (16508) | more than 6 years ago | (#23346242)

I wish there was a +1 Sardonic mod.

Better than Rubik's cube to test 3D skills (2, Insightful)

moteyalpha (1228680) | more than 6 years ago | (#23343670)

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.

Re:Better than Rubik's cube to test 3D skills (1)

tucuxi (1146347) | more than 6 years ago | (#23345006)

Not to mention that there are simple combinations of moves that will guarantee that the cube will get solved. You can cram those in before an interview and voila! an expert 3D problem solver.

A better test for a programmer would be to say "write me a program that solves rubik's cube"... or if you want to test for 3D prowess, ... graphically.

In silico vs classic X-Ray (0)

Anonymous Coward | more than 6 years ago | (#23343698)

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?

look mom, no more cancer (5, Funny)

2TecTom (311314) | more than 6 years ago | (#23343718)

how about a quake mod?

Here's the game URL (1, Redundant)

Trucid (1283736) | more than 6 years ago | (#23343726)

Seems like the editors aren't doing their job. http://fold.it/ [fold.it]

Baker heads up Rosetta (4, Informative)

Krishnoid (984597) | more than 6 years ago | (#23343760)

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).

Re:Baker heads up Rosetta (1)

Digi-John (692918) | more than 6 years ago | (#23343958)

I run Folding@home *because* it doesn't use BOINC. BOINC sucks really really bad

Folding@home, BOINC, FUD (2, Insightful)

Anonymous Coward | more than 6 years ago | (#23345452)

BOINC sucks really really bad
Troll much?

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.

Drugs get Copyrights ya? (3, Interesting)

IronMagnus (777535) | more than 6 years ago | (#23343790)

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? (0)

Anonymous Coward | more than 6 years ago | (#23344122)

From TFA: ...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...
I think you are clueless about how drugs happen. really. It's not an insult, but you are many fathoms beyond your depth of understanding. I mean that with utter sincerity and humility, speaking as someone who knows a bit and so must post anonymously.

There are a lot of links in the chain. Don't worry about who owns the fold for one particular drug. If the 12 year old kid is that good, then he'll have a line of customers till the day he dies. Giving one away won't hurt him.

Re:Drugs get Copyrights ya? (3, Insightful)

Weezul (52464) | more than 6 years ago | (#23344250)

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.

Re:Drugs get Copyrights ya? (1)

Liath (950770) | more than 6 years ago | (#23345058)

Hopefully no one (or everyone) gets the copyright from the drugs, and the researchers are just doing this from the sheer goodness in their hearts that drives them to find the cure to cancer. . .

Unless you consider yourself an input device [patentstorm.us] [patentstorm.com]

How about a way of using a piece of software to create a text document that has never been seen before, but is known to exist?

Right, I think the shark got me after the first paragraph.

Re:Drugs get Copyrights ya? (3, Informative)

laddiebuck (868690) | more than 6 years ago | (#23345186)

This is academia, not industry. We are publicly-funded. Most researchers do not make any money off their discoveries and just get paid from grants. So the poor Indonesian kid probably cannot expect to get rich quick, but at least can be accorded his due share of fame and the benefits arising from that.

Unprecedented (5, Interesting)

Bovius (1243040) | more than 6 years ago | (#23343796)

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.

Re:Unprecedented (2, Funny)

Gat0r30y (957941) | more than 6 years ago | (#23343884)

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.

Re:Unprecedented (2, Informative)

goombah99 (560566) | more than 6 years ago | (#23344134)



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

Re:Unprecedented (1)

raydulany (892228) | more than 6 years ago | (#23344586)

Or The Diamond Age [wikipedia.org] .

Re:Unprecedented (1)

Duncan3 (10537) | more than 6 years ago | (#23345952)

Been happening for a long time, this is just the first one with proteins :) Still cool tho.

I dunno... (0)

Anonymous Coward | more than 6 years ago | (#23343844)

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.

Torrent here: (1, Informative)

Anonymous Coward | more than 6 years ago | (#23343864)

Does not have a Linux client ... (0, Redundant)

jopet (538074) | more than 6 years ago | (#23343918)

Not usable for me.

Re:Does not have a Linux client ... (0)

Anonymous Coward | more than 6 years ago | (#23343996)

Not usable for me
Oh darn. Everyone drop what you are doing to help out this whiner please... K, Thanks...

Re:Does not have a Linux client ... (1)

kel (40052) | more than 6 years ago | (#23344036)

Not usable for me.
The developers will have one ready in a week or so....

Re:Does not have a Linux client ... (1)

jopet (538074) | more than 6 years ago | (#23344160)

Thats good news -- thanks.

Obligatory... (1)

uniquename72 (1169497) | more than 6 years ago | (#23343930)

The adenosine triphosphate is a lie!

Re:Obligatory... (2) (1)

chartreuse (16508) | more than 6 years ago | (#23346262)

Adenosine triphosphate is people!

download is about 50mb (1)

the brown guy (1235418) | more than 6 years ago | (#23344040)

A better game that is sort of similar involves folding eggs around cars, and the protein damages the paint!

Re:download is about 50mb (1)

game kid (805301) | more than 6 years ago | (#23345544)

I remember that game! Grand Theft Amino was a hit, but became rather infamous with the "Hot 11-S-storage" mod.

this could be the next big thing (5, Informative)

rritterson (588983) | more than 6 years ago | (#23344300)

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.

comparison? (0)

Anonymous Coward | more than 6 years ago | (#23345706)

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.
I'm curious about your opinion of the Tanpaku project's approach, which seems to be similar to that of Folding@home and rather "classical". They use (what seems to be) a hybrid molecular dynamics algorithm that greatly reduces 1) the problem complexity, i.e. the number of relevant particles and thus particle-particle interactions, and 2) the timeslices needed to calculate those interactions. Is the gradient descent method a good trade-off of reliability / result precision for computational efficiency?

The problem can be analogized with surveying a landscape. ...
(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.

Umm, this is rosetta@home, not folding@home (2, Informative)

bulletman (254401) | more than 6 years ago | (#23344318)

This game is an offshoot of the rosetta@home [bakerlab.org] effort to model protein folding. Folding@home [stanford.edu] is a separate effort.

It's fun! (2, Informative)

QuantumG (50515) | more than 6 years ago | (#23344532)

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.

Re:It's fun! (2, Informative)

laddiebuck (868690) | more than 6 years ago | (#23345216)

Forgive me, but the whole point is to outdo the computer. Rosetta, the current best algorithm and program (and screensaver) to do protein structure prediction already has sophisticated AI techniques (although the whole problem is essentially a hill-climbing problem), and the whole point is that we want to utilise the most sophisticated visual intelligence known -- humans -- to solve an essentially visual problem. Already very early in the trials, we saw humans, non-biochemists, beat Rosetta, and that pattern has consistently held. Don't be so pessimistic about the project.

Re:It's fun! (1)

QuantumG (50515) | more than 6 years ago | (#23345460)

Oh I'm not. I'm just saying that the level of play that *I* am capable of is so low that I bet even the simplest algorithm could beat me.

Re:It's fun! (1, Informative)

Anonymous Coward | more than 6 years ago | (#23345268)

That's not really true. People have tried genetic algorithms for protein structure prediction, and it's actually non-trivial. The problem is that recombining different parts of proteins is difficult, because the parts that you're trying to combine together aren't compatible. The difficulty of recombining different structures leads to genetic algorithm not performing much better than simulated annealing, an algorithm which Rosetta actually uses.

OMG. This is INSIDEOUS. (I've just played it) (4, Informative)

Danathar (267989) | more than 6 years ago | (#23344590)

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.

Re:OMG. This is INSIDEOUS. (I've just played it) (1)

QuantumG (50515) | more than 6 years ago | (#23345098)

It crashed, that's why I stopped :)

Facebook Genetics Application (0)

Anonymous Coward | more than 6 years ago | (#23344914)

I like the Facebook Genetics Application [genomealberta.ca]

Then there's johnny (4, Funny)

ruiner13 (527499) | more than 6 years ago | (#23344930)

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

QuantumThermoDynamics@home (1)

raftpeople (844215) | more than 6 years ago | (#23345154)

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.

The Protein Gambler (1)

ppanon (16583) | more than 6 years ago | (#23345226)

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.

Nintendo wii! (1)

LiENUS (207736) | more than 6 years ago | (#23345614)

They should port this to the wii, Cant you just imagine it? 4 players competing to fold proteins

Re:Nintendo wii! (1)

corychristison (951993) | more than 6 years ago | (#23346568)

I dunno.

Mario Kart Online is pretty hard to beat. .. damn that game is fun.

Do I read this correctly ? (1)

aepervius (535155) | more than 6 years ago | (#23346386)

"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 ?

pfft (1)

BorgCopyeditor (590345) | more than 6 years ago | (#23346528)

I'm holding out for FoldingFolding@Home Revolution.

Link to movie of gameplay and UW news release (2, Informative)

kendor (525262) | more than 6 years ago | (#23346532)

There is an FLV movie showing the gameplay as well as the University of Washington's news release on the topic at the UW's news site. Link to the news release and contact for media here:


http://uwnews.org/article.asp?articleID=41558 [uwnews.org]

Load More Comments
Slashdot Login

Need an Account?

Forgot your password?

Submission Text Formatting Tips

We support a small subset of HTML, namely these tags:

  • b
  • i
  • p
  • br
  • a
  • ol
  • ul
  • li
  • dl
  • dt
  • dd
  • em
  • strong
  • tt
  • blockquote
  • div
  • quote
  • ecode

"ecode" can be used for code snippets, for example:

<ecode>    while(1) { do_something(); } </ecode>