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Medicine Supercomputing

Google Supercomputers Tackle Giant Drug-Interaction Data Crunch 50

Posted by timothy
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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Google Supercomputers Tackle Giant Drug-Interaction Data Crunch

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  • by gentryx (759438) * on Saturday November 30, 2013 @04:22PM (#45563271) Homepage Journal
    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.
    • by su5so10 (2542686)

      > 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

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

        • by eulernet (1132389)

          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 (Score:4, Insightful)

            by TapeCutter (624760) on Saturday November 30, 2013 @06:18PM (#45563723) Journal
            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.
            • 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!

    • by pepty (1976012)
      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
      • by gentryx (759438) *
        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.
        • by the gnat (153162)

          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.

        • by pepty (1976012)

          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.

          • by pepty (1976012)

            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.

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

    • 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...

      • by stoploss (2842505)

        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!

        • 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.)

    • by Shavano (2541114)

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

  • 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.

    • 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. :-)

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

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

    • 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?

  • is 42.

  • 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?

  • Satan and reefer madness compounds in cannabis...

  • 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

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