Cutting-edge GPU accelerators have helped to achieve a major breakthrough in the battle to fight HIV.
On Wednesday it was widely reported that researchers at the University of Illinois at Urbana-Champaign (UIUC) had determined the precise chemical structure of the HIV capsid, a protein shell that protects the virus's genetic material and is a key to its virulence.
Understanding this structure may hold the key to the development of new and more effective antiretroviral drugs to combat a virus that has killed an estimated 25 million people and infected 34 million more.
But what was not so well publicised was that the researchers had uncovered detail about the capsid structure by running the first all-atom simulation of HIV on the Blue Waters Supercomputer at the National Center for Supercomputing Applications at the University of Illinois, powered by 3,000 NVIDIA Tesla K20X GPU accelerators
“It would have been very difficult to run a simulation of this size without the power of GPU-accelerated supercomputing in the Blue Waters system,” says Klaus Schulten, professor of physics at the University of Illinois. “We started using GPU accelerators more than five years ago, and GPUs have fundamentally accelerated the pace of our research.”
Researchers used a variety of laboratory techniques, including cryo-electron microscopy, cryo-EM tomography, nuclear magnetic resonance spectroscopy and X-ray crystallography – to peer at individual parts of the capsid in revealing detail, or to get a sense of the whole.
But without the computing power provided by the Bluewater System it would have been impossible to piece together the entire HIV capsid – an assemblage of more than 1,300 identical proteins forming a cone-shaped structure – in atomic-level detail.
“GPUs help researchers push the envelope of scientific discovery, enabling them to solve bigger problems and gain insight into larger and more complex systems,” said Sumit Gupta, general manager of the Tesla Accelerated Computing Business Unit at NVIDIA.
“Blue Waters and the Titan supercomputer, the world’s No. 1 open science supercomputer at Oak Ridge National Labs, are just two of many GPU-equipped systems that are enabling the next wave of real-world scientific discovery.”
With the planned addition of more GPUs to the Blue Waters system, UIUC researchers expect to increase simulation times, providing additional insight into the structure and behavior of the HIV capsid.
The capsid has become an attractive target for the development of new antiretroviral drugs, largely due to the discovery that Rhesus monkeys have developed an immunity to HIV through a protein that disrupts capsid functioning.
The capsid is the protein cell of a virus, containing the virus’s genetic material. It protects and “smuggles” the genetic material into the human host cell. Once inside, it uncoats the material and initiates the infection.
No existing HIV drug treatments are designed to target the capsid. However, by providing a better understanding of the structure of the HIV capsid, pharmacologists have a wealth of new information to develop new and potentially more effective antiviral HIV drugs.