Grid models drug effects on smallpox

The screensaver on thousands of volunteers' systems runs a program that tests molecular combinations against the smallpox virus in the search for a cure.

The Defense Department will soon learn whether grid computing can enlist enough idle desktop computing cycles to help in the development of a drug to treat smallpox.

Volunteers for the Smallpox Research Grid Project can download a screensaver from www.grid.org, said Ed Hubbard, chief executive officer of United Devices Inc. of Austin, Texas. As in similar efforts, such as SETI@home, the screensaver periodically downloads a chunk of data from its home server, processes it during idle time and returns the finished work to the server.

Vaccine is currently the only way to prevent smallpox, a potential bioterror agent, but the vaccine can, in rare circumstances, trigger severe side effects. In the event of a terrorist attack with smallpox, physicians would need a drug to treat unvaccinated victims.

'You can't really kill a virus, but you can change the way it behaves in the human body,' Hubbard said.

The screensaver will download simulations of molecules from 35 million drugs to test how they interact with proteins on the surface of a smallpox virus. A successful drug would latch onto the protein targets and disable the virus' reproduction within the human body, Hubbard said.

Secure systems

The project uses United Devices' grid-computing platform, Global MetaProcessor, Hubbard said. It has both a public-key infrastructure and Triple Data Encryption to guard against tampering.

LigandFit software from Accelrys Inc. of San Diego runs the molecular simulations.

Scientists at Oxford University in England contributed a database of 35 million druglike molecules culled from commercial chemical libraries. IBM Corp. contributed several p690 eServers running its DB2 database management system to distribute the screensavers and work, said Michael Nelson, IBM's director of Internet strategy.

IBM is encouraging its employees and customers to use the screensaver. 'It's laying the foundation for potentially exciting new life-science applications,' Nelson said.

United Devices completed a similar anthrax drug grid project after the attacks of Sept. 11, 2001, Hubbard said. IBM and Intel Corp. co-sponsored the anthrax effort and gave the results to DOD, he said. DOD officials then approached United Devices about applying the grid strategy to smallpox treatment, Hubbard said.

The servers will send redundant data packets so researchers can compare completed work from multiple PCs to validate the results, Hubbard said. Overclocking processors on systems might cause floating-point errors that invalidate results.

Answers by spring

Depending on the number of PCs running the screensaver and how long it takes to validate the collected data, the grid team could deliver results to DOD in about two months, Hubbard said.

United Devices and Oxford are also collaborating on a cancer research project, Hubbard said. His company is calling the anti-bioterror efforts the PatriotGrid.

'This is the kind of capability the United States should have in its back pocket, whether it's our grid or someone else's,' he said.

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