Just a few days ago we asked you to contribute your PC's leftover horsepower to help fight the Coronavirus, and while every bit matters, it looks like the Arnold Schwarzenegger of supercomputers is joining the fight: The Oak Ridge National Laboratory (ORNL) just announced that it's bringing in the big guns, tasking Summit with accelerating the process of finding a protein that can bind to the spikes found on the Coronavirus, as reported by HPC Wire. Blocking these spikes would stop the virus from being able to infect lung cells.
Summit employs 220,800 CPU cores, 188,416,000 CUDA cores, 9.2PB of memory, and 250PB of mixed NVRAM/storage for the task.
“Summit was needed to rapidly get the simulation results we needed. It took us a day or two whereas it would have taken months on a normal computer,” said Jeremy Smith, director of UT/ORNL CMB. “Our results don’t mean that we have found a cure or treatment for the Wuhan coronavirus. We are very hopeful, though, that our computational findings will both inform future studies and provide a framework that experimentalists will use to further investigate these compounds. Only then will we know whether any of them exhibit the characteristics needed to mitigate this virus.”
The Summit supercomputer is built by IBM, and currently holds the number one place as the most powerful (publicly ranked) supercomputer in the world. It packs a total of 4,608 nodes, each containing two IBM Power9 CPUs and Six Nvidia Volta GV100 GPUs. For a full technical overview of Summit, you can check out our cheat sheet here.
What's The Science Behind Protein Simulations?
The 2019-nCoV has proteins on its surface called spikes, which trick the ACE2 lung cell surface receptor into letting the virus into the cell and starting a viral infection. One way to stop infection is to find a way to block this protein that resides on the virus, preventing the virus from binding to our cells, and thus rendering it unable to establish an infection. Blocking this protein can be accomplished by binding another protein onto it.
However, proteins can come in an unimaginable amount of shapes, and it will take a very specific protein to bind to the 2019-nCov's spikes.
Thus far, researcher Micholas Smith from the University of Tennessee and ORNL, has used earlier studies to sequence the virus and a virtual model of the Spike protein on the virus. “We were able to design a thorough computational model based on information that has only recently been published in the literature on this virus,” said Micholas Smith.
Using Summit, Smith and his colleagues are simulating the behavior of over 8000 different protein compounds and their ability to bind to the spikes, however, this takes a lot of computer power. Whereas on a powerful computer this process could take months, Summit is able to complete the simulations in mere days.
Up until now, Smith has found 77 different small-molecule drug compounds that are worth further study.
"Using Summit, we ranked these compounds based on a set of criteria related to how likely they were to bind to the S-protein spike,” Smith explained.
Eventually, once a protein is found that can bind to the 2019-nCov's spikes with a high success rate, it can be synthesized into a vaccine.