A Canadian disease researcher has provided some of the biological expertise needed to power a grid computing project that could speed a cure for small pox.
IBM Canada Wednesday said it had completed a six-month initiative that also involved the Robarts Research Institute at the University of Western Ontario and grid computing software provider United Devices, among many others. The project, which was designed to isolate the molecules that can be considered lead candidates for further drug research, was powered through millions of computers. Users downloaded software at grid.org and their computer power was harnessed while the machines were idle.
A small pox vaccine already exists but doesn’t work on patients who have already been exposed to the virus and can cause adverse reactions in others.
Grant McFadden, co-director of the BioTherapeutics Research Group at Robarts and Western’s Canada Research Chair in Molecular Virology, said the grid allowed researchers to screen close to 35 million molecules against small pox in a sort of computer simulation called in-silico. McFadden, whose research looks at the kinds of strategies pox viruses use to create diseases, said he had never encountered grid computing prior to the project.
“”I’m quite intrigued by it,”” he said. “”The screening part of it — the heavy lifting they had to do to fit all of these 50 million compounds into the target sites was quite impressive. The end result is that within about three or months of the grid working away at it, they were able to get a hierarchy of these 35 million compounds.””
McFadden’s role was primarily to help choose the right targets for the screening process.
“”These viruses take a couple hundred proteins; there’s innumerable numbers of interface sites on all of the proteins, so there’s literally thousands of domains the proteins could pick,”” he said.
Tim Williams, senior product marketing manager at United Devices in Austin, Tex., said the project was sponsored by IBM and the United States Department of Defense — the agency that had worked with United Devices on a similar project involving Anthrax.
“”When it came to small pox, the structure wasn’t as well understood (as Anthrax),”” said Williams, whose firm partnered with another company, Evotec OAI, to produce models of an unknown region of the disease targets. “”There was much work needed to be done up front in order to actually do the screening.””
McFadden said the top candidates from the in-silico screening can now be tested in-vitro in the lab. Those that make it through that level of screening can then be tested against virus-infected cells. “”The (test) itself is fairly fast,”” he said. “”The rate-limiting thing is to acquire those thousand-plus candidates, because they’re in different databases, they’re in different libraries. I would think the next level of complexity is the logistics of getting the compounds together.””
Williams said projects like this one, which attracted computer users in more than 190 countries, help advance the cause of grid computing to assist in compute-intensive research areas.
“”When people see this, they like to try and contribute,”” he said. “”As far as results, it may be a couple of years before we find out if our work was actually able to produce anything.””
The U.S. Department of Defense saw the results last month, Williams said, and will take the project to the next stage of research. Accelrys, the University of Oxford, Sloan-Kettering Cancer Center and Essex University also contributed to the project.