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Google Supercomputers Tackle Giant Drug-Interaction Data Crunch

timothy posted about 10 months ago | from the more-cubbies-for-more-index-cards dept.

Medicine 50

ananyo writes "By analysing the chemical structure of a drug, researchers can see if it is likely to bind to, or 'dock' with, a biological target such as a protein. Researchers have now unveiled a computational effort that used Google's supercomputers to assesses billions of potential dockings on the basis of drug and protein information held in public databases. The effort will help researchers to find potentially toxic side effects and to predict how and where a compound might work in the body. 'It's the largest computational docking ever done by mankind,' says Timothy Cardozo, a pharmacologist at New York University's Langone Medical Center, who presented the project at the US National Institutes of Health's High Risk–High Reward Symposium in Bethesda, Maryland. The result, a website called Drugable, is still in testing, but it will eventually be available for free, allowing researchers to predict how and where a compound might work in the body, purely on the basis of chemical structure."

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Timmay! (0, Troll)

Anonymous Coward | about 10 months ago | (#45563241)

To 'assesses'?

Timmay are good at grammars!

Which supercomputer? (2)

gentryx (759438) | about 10 months ago | (#45563271)

TFA is light on the technical details, so I wonder if they've really been using a supercomputer or rather "a giant heap of ordinary computers". IIRC Google has more of the latter and fewer of the former.

Re:Which supercomputer? (2)

su5so10 (2542686) | about 10 months ago | (#45563355)

> IIRC Google has more of the latter and fewer of the former.

Yes, you are correct. More details here:

http://research.google.com/university/exacycle_program.html [google.com]

"The best projects will have a very high number of independent work units, a high CPU to I/O ratio, and no inter-process communication (commonly described as Embarrassingly or Pleasantly Parallel). The higher the CPU to I/O rate, the better the match with the system. Programs must be developed in C/C++ and compiled via Native Client. Awardees will be able to consult an on-site engineering team."

Native Client: http://en.wikipedia.org/wiki/Google_Native_Client [wikipedia.org]

Re:Which supercomputer? (2)

buchner.johannes (1139593) | about 10 months ago | (#45563367)

they could use BOINC too -- its the largest supercomputer on earth :)

Re:Which supercomputer? (2)

eulernet (1132389) | about 10 months ago | (#45563509)

The fastest supercomputer (http://en.wikipedia.org/wiki/Tianhe-2) runs at 33.86 petaflops, while Boinc currently runs at 8.26 petaflops (http://boincstats.com/en/stats/-1/project/detail).

3 years ago, Google's computers were used to solve Rubik's cube:
http://cube20.org/ [cube20.org]

We can suppose that combined Google servers are above 33Pflops.

The Oracle (3, Insightful)

TapeCutter (624760) | about 10 months ago | (#45563723)

Watson is planning to sit for his US medical license soon, next year IBM will be renting "instances" of Watson to independent developers. Since it beat the human Jeopardy champs a couple of years ago Watson has shrunk from 20 tons (including air-con) to a 50kg "beer fridge" running Linux, and it's also 2.6 times faster.

These machines are what IBM calls "cognitive computing", they can find answers in data that we didn't know were there. In Watsons case the data is general knowledge (AKA common sense), in this case the data is biomedical. There are lots of video's on you tube about Watson but most are cheesy IBM "what we can do for you" infomercials, the talks from the actual developers and the Jeopardy stunt are worth watching.

I know I keep banging on about IBM's Watson in my posts, and although I contracted to them in the 90's I'm not a shill, I'm a degree qualified computer scientist with 20+ yrs as a commercial developer. I was born the year after sputnik was launched, the technological and scientific progress in my lifetime is unparalleled in human history. I really believe that the "AI" developments we are seeing with HPC today are a revolution like none before, machines that are "smarter" than their creators. It already to the point that no major (physical) engineering project is conducted without the aid of computer models, in fact it's basically impossible to design a modern cpu with first having a modern cpu.

The ancient myth of the Oracle has come to life as a flat screen monitor, it will change everything in a single generation, hopefully in a good way.

Re: The Oracle (2)

DigiShaman (671371) | about 10 months ago | (#45564031)

Oh, it will change everything all right. But not for the better. It will be used as a tool by man against mankind . It will be a tool of oppression by the oppressors.

Watson will be used as a tool like any other. Just look how our advanced tools are being used against us! Be it political divide and conquer, oppression, tyranny, or war; man is his own worst enemy!

Re: The Oracle (1)

Pseudonym Authority (1591027) | about 10 months ago | (#45565147)

Things aren't so terrible. Just relax for a second and broaden the criteria by which you judge.

Re:Which supercomputer? (2)

pepty (1976012) | about 10 months ago | (#45563423)

Garbage in, garbage out. The architecture of the computer doesn't matter much if the forcefield (the set of equations used to model the interaction between the atoms in the drug, the atoms in the protein, and the atoms in the environment) isn't accurate enough. So far they aren't. This set up seems to have found the known and several putative binding sites for clozapine, but the article doesn't say anything about false positives/false negatives it reported. The setup also pre-selects the binding sites to be studied, which makes me think it would miss a lot of interactions that happen elsewhere on the proteins. The article also points out that Pharma companies have been doing the same type of calculations for years, just on fewer drugs. Pharma haven't managed to create in silico predictions of pre clinical trials yet, let alone clinical trials. This is work worth doing, but like Folding At Home the results are easy to over-hype.

Re:Which supercomputer? (1)

gentryx (759438) | about 10 months ago | (#45563469)

The advantage of (real) Supercomputers is that they can tackle large scale simulations (instead of large numbers of small scale simulations, which is what "Folding@Home" and co. do). Would the quality of the predictions go up if they used a more accurate (and thus computationally complex) model of the forcefield? AFAIK DE Shaw Research [deshawresearch.com] is building their "Anton" line of supercomputers for the simulation of molecular dynamics.

Re:Which supercomputer? (1)

the gnat (153162) | about 10 months ago | (#45564367)

Would the quality of the predictions go up if they used a more accurate (and thus computationally complex) model of the forcefield? AFAIK DE Shaw Research [deshawresearch.com] is building their "Anton" line of supercomputers for the simulation of molecular dynamics.

True, but they've almost entirely been using simple forcefields (with some of their own improvements); the supercomputer is so they can run the MD simulations for orders of magnitude longer.

Re:Which supercomputer? (1)

pepty (1976012) | about 10 months ago | (#45566415)

The advantage of (real) Supercomputers is that they can tackle large scale simulations (instead of large numbers of small scale simulations, which is what "Folding@Home" and co. do). Would the quality of the predictions go up if they used a more accurate (and thus computationally complex) model of the forcefield? It would certainly help when it comes to electrostatics: solving the full nonlinear Poisson Boltzmann equation (as opposed to approximations) for all the atoms in the solvent, protein, and drug molecules is a bitch; doing it several billion times during a simulation is ... bitch x 10^9. The problem right now is that predictions from first principles of much simpler systems still tend to get a lot of things wrong: they're really only beginning to get a handle on how water works at this scale.

Re:Which supercomputer? (1)

pepty (1976012) | about 10 months ago | (#45566439)

Oops

The advantage of (real) Supercomputers is that they can tackle large scale simulations (instead of large numbers of small scale simulations, which is what "Folding@Home" and co. do). Would the quality of the predictions go up if they used a more accurate (and thus computationally complex) model of the forcefield?

It would certainly help when it comes to electrostatics: solving the full nonlinear Poisson Boltzmann equation (as opposed to approximations) for all the atoms in the solvent, protein, and drug molecules is a bitch; doing it several billion times during a simulation is ... bitch x 10^9. The problem right now is that predictions from first principles of much simpler systems still tend to get a lot of things wrong: they're really only beginning to get a handle on how water works at this scale.

Re:Which supercomputer? (0)

Anonymous Coward | about 10 months ago | (#45563471)

In addition researchers are way overconfident in their tissue expression and function data. Alot of that stuff is based off like 3 western blots and 10 rats.

Re:Which supercomputer? (0)

Anonymous Coward | about 10 months ago | (#45567357)

spot on. And further more, the article suggest they are "data mining" not docking anything...

What a lot of people do not realise is we can design anything we like on a computer. But making it (synthesis) in sufficient quantities is currently at the limit of our understanding. Hence, the process of "drug discovery" is just that. Try known compounds against a range of objective(!) biochemical and clinical parameters, until you get a few "leads", which can then go through the FDA process. Computers can help to reduce the number of false starts.

The Anton supercomputer is a special purpose machine to solve extremely long time simulations (1ms, 10^12 timesteps), with a pair-potential (2 particle interaction) and electrostatics. It does the 3D FFT for calculating the electrostatic forces VERY fast (32x32x32 4us). They published it too.

Re: Which supercomputer? (0)

Anonymous Coward | about 10 months ago | (#45563557)

If it giant all working together in health sector, we might see good progress soon. To find new medicine, and others

Re:Which supercomputer? (1)

CAPSLOCK2000 (27149) | about 10 months ago | (#45564157)

What's the difference? Most supercomputers are in fact a cluster of more or less normal computer parts.

Re:Which supercomputer? (1)

Areyoukiddingme (1289470) | about 10 months ago | (#45564587)

I do wish they wouldn't be so damn sloppy with language. Google datacenters host what can be described as a supercluster. Supercomputers have much higher interconnection between nodes and much faster interconnects.

Words! They mean things!

Fucking journalists...

Re:Which supercomputer? (1)

stoploss (2842505) | about 10 months ago | (#45565389)

Words! They mean things!

No, they don't—we now live in a post-semantic era.

I found out the other day that "figuratively" is now an accepted definition for "literally". Post-semantic... how else can one describe a situation where $TERM == NOT $TERM? Furthermore, "figuratively" does not currently mean "literally", so the symmetry of equality is broken. This is just madness.

You maniacs! You blew semantics up! Ah, damn you! God damn you all to hell!

Re:Which supercomputer? (1)

Areyoukiddingme (1289470) | about 10 months ago | (#45565945)

Heh. Yeah, I found that out a few months ago. I got half the office going on the subject. (Rather sadly. Programmers think they're funny when often they're not.)

Re:Which supercomputer? (1)

Shavano (2541114) | about 10 months ago | (#45565579)

Doesn't matter. This task is ideally suited for parallel processing.

Why limit it to drugs? (0)

Anonymous Coward | about 10 months ago | (#45563275)

Why limit the purpose of the site to drugs? Can we stick in molecules found in foods?

Re:Why limit it to drugs? (1)

Desler (1608317) | about 10 months ago | (#45563287)

Because the person running it is a pharmocologist and thus that would be their area of interest?

Re:Why limit it to drugs? (0)

Anonymous Coward | about 10 months ago | (#45563497)

Yeah, I hear that, but my point is that the same techniques and infrastructure work for both.

Think about ending the controveries (one way or the other) about GMO foods, pesticides, hormones, common pollutants, etc.

Re:Why limit it to drugs? (0)

Anonymous Coward | about 10 months ago | (#45563947)

The research reported, and what you suggest, strikes me as one of the really useful things to do with a bunch of computing power. As it stands, I'm hoping this project and its follow-ons can make a real difference with the drug interaction stuff; not only can they harm or kill a patient but they're often unpleasant at best. Also, if this could reduce just the side effects of many drugs it would be a big help.

Re:Why limit it to drugs? (1)

Shavano (2541114) | about 10 months ago | (#45565603)

That would be useless. Those fights are dominated by an argument between those who use the products for profit on the one hand and True Believers on the other.

Re: Why limit it to drugs? (1)

Anonymous Coward | about 10 months ago | (#45564763)

Pharmacology would include any molecule that interacts with the bodies processes.

Re:Why limit it to drugs? (1)

TapeCutter (624760) | about 10 months ago | (#45563753)

There're often the same thing, eg: Aspirin is found in apples but it's easier to extract from Willow bark or coal.

Re:Why limit it to drugs? (1)

fuzzyfuzzyfungus (1223518) | about 10 months ago | (#45564507)

Why limit the purpose of the site to drugs? Can we stick in molecules found in foods?

Probably because (unless you are willing to accept high-school-chem levels of oversimplification, and probably even if you are) computational chemistry is not exactly a problem that has any difficulty consuming all the computational resources we could possibly throw at it (unless you count problems with scaling, which I suspect that it has in spades, just to make computing with cheap interconnect less practical).

Drugs have the virtue of being (relatively) simple compared to most naturally occurring materials and (ideally) are fairly narrowly targeted. Both are significant virtues if you want to keep the scope of your simulation within the scope of the remotely possible...

Computer predictions (1, Funny)

TheloniousToady (3343045) | about 10 months ago | (#45563341)

Predicting when proteins will dock with targets is fine, but I'll really be impressed if Google's "supercomputers" can predict when users will dock with healthcare.gov.

Re:Computer predictions (1)

TheloniousToady (3343045) | about 10 months ago | (#45563807)

Sorry if that offended anyone, but it was intended as a joke, not a troll. (I never know how my jokes will go over here - some have been well received, some less so, but I've never had one marked as a troll before.)

BTW, this one also isn't a troll, it's just an explanation. :-)

Re:Computer predictions (0)

Anonymous Coward | about 10 months ago | (#45566955)

Suck my dick.

Re:Computer predictions (0)

Anonymous Coward | about 10 months ago | (#45569123)

OK, I'll sick my duck.

Google supercomputer? (-1)

Anonymous Coward | about 10 months ago | (#45563479)

What? Where would the worlds largest advertising company need supercomputers for? You need a supercomputer to sell ads these days?

"docking", hee hee (1)

SuperBanana (662181) | about 10 months ago | (#45563505)

http://www.urbandictionary.com/define.php?term=docking [urbandictionary.com]

Yes, I'm fifteen. Admittedly, a rather-well-sexually-educated fifteen...

Re:"docking", hee hee (1)

ColdWetDog (752185) | about 10 months ago | (#45563657)

A fifteen year old with a six digit UID?

What happened? Your parent's got bored with you and set you in front of Slashdot as a toddler?

The answer (1)

Mononoke (88668) | about 10 months ago | (#45563547)

is 42.

The real important questions (1)

nospam007 (722110) | about 10 months ago | (#45563609)

I see nobody asked the real important questions.

Are they also checking if you can get high from a substance?
Is somebody going to leak that list?

Re:The real important questions (3, Informative)

ColdWetDog (752185) | about 10 months ago | (#45563673)

I see nobody asked the real important questions.

Are they also checking if you can get high from a substance?
Is somebody going to leak that list?

No need to do that. The Federal Government has gone to great expense and trouble to compile this exhaustive list [usdoj.gov] of drugs that can get all the blinky lights in your brain going.

Re:The real important questions (0)

Anonymous Coward | about 10 months ago | (#45563903)

I had some idea it was a long list, but, wow.

Saw a few things I met way back when, MMDA, and the delta-9 THC - the latter we got in roundabout fashion from a lab at U of Mich. (I found the high to be cold and clinical - with few or no harmonics and a thin undercurrent of dissonance. It was a 'clean' high, somewhat intense, and not entirely pleasant - that bit seemed to vary with the individual or was beneath their threshold of reporting. It didn't have the warmth or relaxed feeling of weed.)

Re:The real important questions (1)

fuzzyfuzzyfungus (1223518) | about 10 months ago | (#45564677)

The list isn't actually exhaustive: we have the "Federa Analog Act [usdoj.gov] " for that...

Any wanna take bets that they'll find (1)

future assassin (639396) | about 10 months ago | (#45563655)

Satan and reefer madness compounds in cannabis...

For the Results of an Experimental Approach (2)

Streetlight (1102081) | about 10 months ago | (#45563829)

take a look at the article in Chemical and Engineering News (C&EN), Nov. 25, 2013, page 7, about a relatively small molecule that interacts with a mutant protein associated with cancer. A very nice x-ray structure is shown with the inhibiting molecule covalently bonded to the protein. The NIH is putting up $10 to further this kind of work. On page 9 of the same issue is another interesting article regarding experimental cancer work and the effect of bacteria in the gut on chemotherapy effectiveness. C&EN should be available in most university libraries.

Re:For the Results of an Experimental Approach (0)

Anonymous Coward | about 10 months ago | (#45564247)

holy shit $10 where do they get all this money

Re:For the Results of an Experimental Approach (1)

Streetlight (1102081) | about 10 months ago | (#45565473)

Ooops! $10 MILLION.

Google Jobs (-1, Offtopic)

Rosie Amber (3449935) | about 10 months ago | (#45566227)

just before I looked at the paycheck 4 $6482, I didnt believe that my neighbour woz like they say realie earning money parttime online.. there best friend has been doing this 4 only about eight months and recently took care of the dept on their home and bourt themselves a Lotus Elan. navigate to this site============> www.blue48.com =============

Google Jobs (0)

Rosie Amber (3449935) | about 10 months ago | (#45566245)

justt before I looked at the paycheck 4 $6482, I didnt believe that my neighbour woz like they say realie earning money parttime online.. there best friend has been doing this 4 only about eight months and recently took care of the dept on their home and bourt themselves a Lotus Elan. navigate to this site============> www.blue48.com =============

Whoopie shit! More F'ing Drugs... *facepalm* (0)

Anonymous Coward | about 10 months ago | (#45566557)

The nation is already dying off like flies from taking the existing Rx death pills and they want to help make more? Definitely money in it for them.

Keep it Clean! :D

(Learn how to medicate yourself with canna pills at TheCleanGame [.] Net

For which unit of "largest"? (0)

Anonymous Coward | about 10 months ago | (#45566705)

"It's the largest computational docking ever done by mankind"
What does this mean? Largest carries no meaning without some kind of unit.
Largest in terms of teraflops (and where does BOINC with its 8200TFlops, a lot of which is docking, stand compared to this?)
Largest in terms of number of machines involved?
Largest in terms of the number of involved scientists?
Largest in terms of the number of proteins, the docking search space?

Docking (0)

Anonymous Coward | about 10 months ago | (#45566969)

as long as current docking algorithms are used these will just predictions with no real world application, STOP hype science!

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