Amazon, Cycle Computing Create Supercomputer for Drug Discovery, Cancer Research
Supercomputing and big data have taken yet another step forward in leading to new treatment for cancer.
Schr dinger, a company that offers molecular-modeling and drug-design software, and Nimbus Discovery are using Cycle Computing's 50,000-core supercomputer to run a virtual screen to find a protein target responsible for cancer.
Schr dinger helps fund the work of Nimbus, which performs drug discovery and molecular modeling.
Cycle Computing announced the creation of the supercomputer cluster, code-named Naga, at the Amazon Web Services summit in New York City on April 19.
AWS' cluster of servers power the research in a cloud environment. The CycleCloud high-performance computing (HPC) software brought the cluster to the supercomputing level.
"We take those servers and turn them into a working, functioning supercomputer," Jason Stowe, founder and CEO of Cycle Computing, told eWEEK.
Schr dinger offers Glide, a computational docking application that performs the screening of compound libraries as researchers try to identify proteins that may have an effect on cancer activity. These discoveries can lead to the development of potential treatment.
"What they're trying to do is find molecules that would fit into the target on this protein, much like a lock-and-key kind of scenario," said Stowe.
As a mapping application, Glide allowed researchers to virtually screen 21 million molecule conformations against a possible cancer target. The software simulates the placement of a molecule into the protein, said Stowe.
"In order to do that in a reasonable period of time, they need multiple machines, and that's essentially what a high-performance-supercomputing cluster is used for," Stowe explained.
Following computational testing, Schr dinger and Nimbus are physically testing the molecules in a lab.
"We will be purchasing and assaying the compounds that came from this virtual screen to confirm that indeed better science gives better results," Ramy Farid, president of Schr dinger, told eWEEK in an email. "It's hard to imagine that this will not be the case, but we have to do the experiment to confirm it."
Researchers also used the supercomputing vendor's CycleServer software to perform analytics, diagnose performance and manage the scientific workflow for the project.
Researchers completed the run in less than three hours compared with traditional methods, Stowe noted.
"Essentially, they're taking months off of this process," he said. "If you were to try and run this in-house , you would either miss drugs because you did it the old way or essentially, you'd wait considerable periods of time--a couple of months to get the results back--and then have to sift through them."
The computations cost $4,900 per hour at peak without up-front capital to access the computing capabilities through the cloud, Cycle reported in a blog post. An in-house supercomputer would cost tens of millions of dollars to power, cool and manage, according to Cycle.
"It would take a considerably longer period of time, so they'd never be able to run it in house," said Stowe.
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