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Google Supercomputers Tackle Giant Drug-Interaction Data Crunch
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."
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
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!
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.
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