Do you play a little more “Call of Duty: Black Ops II” than you’d care to admit? Got a ridiculously powerful GPU? When you’re not defending your nation from bad guys, maybe you’ll want to donate a little of that computing power to help advance the fight against AIDS.
Using GPUGrid.net – a volunteer distributed-computing effort that uses spare time on the GPUs of thousands of volunteers – Spanish researchers have made an important breakthrough in the quest to better understand HIV, the virus that causes AIDS.
Bioinformaticians at IMIM (Hospital del Mar Medical Research Institute) and UPF (Pompeu Fabra University) in Barcelona said today that, for the first time, they have simulated the behavior of the initial crucial step in the HIV maturation process.
Modeling How HIV Matures
The action of a protein called ‘HIV protease’ is responsible for the initial step of the whole HIV virus maturation process, which enables the virus to become infectious.
It turns out, the HIV protease acts like a pair of scissors. These “scissors proteins,” cuts the long chain of connected proteins that form HIV into individual proteins. These individual proteins, or virons, then take viral genomes from one cell to another.
Using GPU-accelerated software called ACEMD, researchers showed how the first HIV “scissors proteins” can cut themselves out from within the middle of these poly-protein chains, beginning the infectious phase of HIV.
By providing this new visibility into how the HIV protease behaves, bio-tech researchers can potentially design new antiretroviral drugs to halt the HIV maturation process to stop it from becoming infectious.
From Blasting Aliens to Battling HIV
The Barcelona researchers achieved this breakthrough by harnessing the power of thousands of NVIDIA GPU accelerators on a network of individual computers—not unlike one of the high-end PC gaming rigs you have on your desk at home.
This approach gave them access to a virtual supercomputer, giving them access to 10 times more computational performance than with comparable CPU-based systems. That’s a level of processing power that once was only available on dedicated, multi-million dollar supercomputers.
With this tremendous computing power at their disposal, the researchers were able to run thousands of complex computer simulations of HIV protease, each for hundreds of nanoseconds for a total of almost a millisecond. That gives them a very high-probability that their simulation represented real-world behaviors.
Simulations of this length and complexity would have been unfeasible to achieve using a computing system based on CPUs alone.
These findings have been published in the latest edition of Proceedings of the National Academy of Sciences of the United States of America (PNAS).
So, next time you fire up “Assassin’s Creed III” or another PC game that screams for massive GPU performance, think of how cool it is that the very same technology is helping solve some of society’s biggest problems.
Pictured, above, the HIV protease protein.
Tagged: AIDS, GPGPU, gpu, HIV, IMIM (Hospital del Mar Medical Research Institute), UPF (Pompeu Fabra University)
