Google Supercomputers Tackle Giant Drug-Interaction Data Crunch

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Google Supercomputers Tackle Giant Drug-Interaction Data Crunch

Posted by timothy on Saturday November 30, 2013 @09:06AM from the more-cubbies-for-more-index-cards dept.

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! by Anonymous Coward · 2013-11-30 09:18 · Score: 0, Troll

To 'assesses'?
Timmay are good at grammars!
Which supercomputer? by gentryx · 2013-11-30 09:22 · Score: 2

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.

--
Computer simulation made easy -- LibGeoDecomp
1. Re:Which supercomputer? by su5so10 · 2013-11-30 09:37 · Score: 2
  
  > 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
  "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
2. Re:Which supercomputer? by buchner.johannes · 2013-11-30 09:40 · Score: 2
  
  they could use BOINC too -- its the largest supercomputer on earth :)
  
  --
  NB: The message above might reflect my opinion right now, but not necessarily tomorrow or next year.
3. Re:Which supercomputer? by pepty · 2013-11-30 09:51 · Score: 2
  
  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.
4. Re:Which supercomputer? by gentryx · 2013-11-30 10:02 · Score: 1
  
  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 is building their "Anton" line of supercomputers for the simulation of molecular dynamics.
  
  --
  Computer simulation made easy -- LibGeoDecomp
5. Re:Which supercomputer? by Anonymous Coward · 2013-11-30 10:03 · Score: 0
  
  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.
6. Re:Which supercomputer? by eulernet · 2013-11-30 10:12 · Score: 2
  
  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/
  We can suppose that combined Google servers are above 33Pflops.
7. Re: Which supercomputer? by Anonymous Coward · 2013-11-30 10:25 · Score: 0
  
  If it giant all working together in health sector, we might see good progress soon. To find new medicine, and others
8. Re:Which supercomputer? by CAPSLOCK2000 · 2013-11-30 12:29 · Score: 1
  
  What's the difference? Most supercomputers are in fact a cluster of more or less normal computer parts.
9. Re:Which supercomputer? by the+gnat · 2013-11-30 12:57 · Score: 1
  
  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.
10. Re:Which supercomputer? by Areyoukiddingme · 2013-11-30 13:32 · Score: 1
  
  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...
11. Re:Which supercomputer? by stoploss · 2013-11-30 15:41 · Score: 1
  
  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!
12. Re:Which supercomputer? by __aaltlg1547 · 2013-11-30 16:13 · Score: 1
  
  Doesn't matter. This task is ideally suited for parallel processing.
13. Re:Which supercomputer? by Areyoukiddingme · 2013-11-30 17:27 · Score: 1
  
  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.)
14. Re:Which supercomputer? by pepty · 2013-11-30 19:28 · Score: 1
  
  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.
15. Re:Which supercomputer? by pepty · 2013-11-30 19:32 · Score: 1
  
  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.
16. Re:Which supercomputer? by Anonymous Coward · 2013-12-01 01:21 · Score: 0
  
  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.
Why limit it to drugs? by Anonymous Coward · 2013-11-30 09:22 · Score: 0

Why limit the purpose of the site to drugs? Can we stick in molecules found in foods?
1. Re:Why limit it to drugs? by Desler · 2013-11-30 09:24 · Score: 1
  
  Because the person running it is a pharmocologist and thus that would be their area of interest?
2. Re:Why limit it to drugs? by Anonymous Coward · 2013-11-30 10:09 · Score: 0
  
  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.
3. Re:Why limit it to drugs? by TapeCutter · 2013-11-30 11:27 · Score: 1
  
  There're often the same thing, eg: Aspirin is found in apples but it's easier to extract from Willow bark or coal.
  
  --
  And did you exchange a walk on part in the war for a lead role in a cage? - Pink Floyd.
4. Re:Why limit it to drugs? by Anonymous Coward · 2013-11-30 12:00 · Score: 0
  
  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.
5. Re:Why limit it to drugs? by fuzzyfuzzyfungus · 2013-11-30 13:19 · Score: 1
  
  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...
6. Re: Why limit it to drugs? by Anonymous Coward · 2013-11-30 13:59 · Score: 1
  
  Pharmacology would include any molecule that interacts with the bodies processes.
7. Re:Why limit it to drugs? by __aaltlg1547 · 2013-11-30 16:17 · Score: 1
  
  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.
Computer predictions by TheloniousToady · 2013-11-30 09:34 · Score: 1, Funny

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.
1. Re:Computer predictions by TheloniousToady · 2013-11-30 11:39 · Score: 1
  
  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. :-)
2. Re:Computer predictions by Anonymous Coward · 2013-11-30 22:42 · Score: 0
  
  Suck my dick.
3. Re:Computer predictions by Anonymous Coward · 2013-12-01 06:48 · Score: 0
  
  OK, I'll sick my duck.
"docking", hee hee by SuperBanana · 2013-11-30 10:11 · Score: 1

http://www.urbandictionary.com/define.php?term=docking
Yes, I'm fifteen. Admittedly, a rather-well-sexually-educated fifteen...

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Please help metamoderate.
1. Re:"docking", hee hee by ColdWetDog · 2013-11-30 10:53 · Score: 1
  
  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?
  
  --
  Faster! Faster! Faster would be better!
The answer by Mononoke · 2013-11-30 10:21 · Score: 1

is 42.

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NetInfo connection failed for server 127.0.0.1/local
The real important questions by nospam007 · 2013-11-30 10:38 · Score: 1

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?
1. Re:The real important questions by ColdWetDog · 2013-11-30 10:56 · Score: 3, Informative
  
  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 of drugs that can get all the blinky lights in your brain going.
  
  --
  Faster! Faster! Faster would be better!
2. Re:The real important questions by Anonymous Coward · 2013-11-30 11:53 · Score: 0
  
  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.)
3. Re:The real important questions by fuzzyfuzzyfungus · 2013-11-30 13:42 · Score: 1
  
  The list isn't actually exhaustive: we have the "Federa Analog Act" for that...
Any wanna take bets that they'll find by future+assassin · 2013-11-30 10:52 · Score: 1

Satan and reefer madness compounds in cannabis...

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by TheSpoom (715771) Uncaring Linux user here. I have nothing to add to this but please continue. *munches popcorn*
The Oracle by TapeCutter · 2013-11-30 11:18 · Score: 3, Insightful

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.

--
And did you exchange a walk on part in the war for a lead role in a cage? - Pink Floyd.
1. Re: The Oracle by DigiShaman · 2013-11-30 12:11 · Score: 2
  
  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!
  
  --
  Life is not for the lazy.
2. Re: The Oracle by Pseudonym+Authority · 2013-11-30 14:59 · Score: 1
  
  Things aren't so terrible. Just relax for a second and broaden the criteria by which you judge.
For the Results of an Experimental Approach by Streetlight · 2013-11-30 11:42 · Score: 2

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.

--
In a time of universal deceit, telling the truth is a revolutionary act. George Orwell
1. Re:For the Results of an Experimental Approach by Anonymous Coward · 2013-11-30 12:41 · Score: 0
  
  holy shit $10 where do they get all this money
2. Re:For the Results of an Experimental Approach by Streetlight · 2013-11-30 15:55 · Score: 1
  
  Ooops! $10 MILLION.
  
  --
  In a time of universal deceit, telling the truth is a revolutionary act. George Orwell
Whoopie shit! More F'ing Drugs... *facepalm* by Anonymous Coward · 2013-11-30 20:11 · Score: 0

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"? by Anonymous Coward · 2013-11-30 21:05 · Score: 0

"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 by Anonymous Coward · 2013-11-30 22:48 · Score: 0

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