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Computer Aid Sought to Find Virus Cure

Posted on: Thursday, 23 August 2007, 06:10 CDT

By Carrie Peyton Dahlberg, The Sacramento Bee, Calif.

For those who want to do more than wear mosquito repellant and drain standing water, researchers are offering a new way to fight West Nile virus: Volunteer your computer to help seek a cure.

A project that will use personal computers to analyze key vulnerabilities of the virus is being launched this week, the latest in a string of scientific and medical research harnessing the Internet.

All rely on the same, simple idea: borrowing a little time from a lot of idle computers.

"If millions of us around the world are able to join up and provide this kind of computing power, we really can make a difference," said Clark Kelso, Gov. Schwarzenegger's chief adviser on information technology.

The West Nile effort may hold a special appeal for communities like Sacramento, where pesticide spraying to combat the virus has been a polarizing issue.

"It would be a big boost for us" if a treatment could be found some day for West Nile diseases, said Gary Goodman, assistant manager of the Sacramento-Yolo Mosquito and Vector Control District.

California health officials report eight deaths linked to West Nile virus so far this year, and 137 cases of humans infected with the virus. The Sacramento-Yolo district has reported four human cases, and the governor has listed the area as "high risk" for the virus.

While a treatment might not change the vector district's surveillance and prevention work, Goodman said, "it would be a great thing for public health."

Every department of state government should seriously consider letting employees sign up for such public interest computing, which has no impact on a computer's primary tasks, said Kelso.

For years, Kelso has opened up his home and work computers to everything from AIDS research to the search for extraterrestrial life, but the West Nile project carries a poignant, personal connection.

His wife's sister was hospitalized for nine months, much of the time on a respirator, with West Nile encephalitis.

"Until it hits close to you, you don't fully appreciate what can happen," said Kelso, whose sister-in-law is now recovering slowly at home in Nevada.

Most people bitten by a mosquito that carries West Nile virus never know it, but some develop intense flu-like symptoms and a few come down with encephalitis, meningitis or paralysis. For a tiny minority, the disease is fatal.

Researchers have zeroed in on a few compounds that stop growth of the virus in lab dishes, and some are being tested on mice, said Stan Watowich, a biochemistry professor at the University of Texas.

Yet in the effort to develop new drugs, a few promising compounds are not enough, he said. Some may turn out to have dangerous side effects in humans. Others may attack one form of a virus but leave a variant unscathed.

Watowich and fellow researchers are hoping their new Internet project will identify dozens more compounds that could attack a protein in viruses that cause West Nile, dengue fever, yellow fever, hepatitis C and other diseases.

They are focusing on a protein critical to the viruses' replication. Computers will be used to model how that protein reacts to a vast electronic library of other molecules. Those that bind most tightly to the protein's active site will essentially disable it, preventing the virus from reproducing.

Watowich estimates the analysis will require comparing about 6.5 million molecules to 50 different variants of the protein.

Such comparisons "would take dozens and dozens of years on very large computers," assuming researchers could even get that much supercomputer time, he said.

Yet because the work can be broken into millions of separate tasks, it can be shared by computers everywhere, each taking on one comparison at a time.

With that approach, dubbed "Discovering Dengue Drugs -- Together," Watowich figures the whole thing should take about a year.

He and others who use such "distributed" or "grid" computing to aid drug discovery stress that it is only the first step. It produces leads that can be followed up in laboratory, animal and human testing.

"Drug design is a process that takes 10 or 15 years," said Vijay Pande, a Stanford chemistry and structural biology professor who developed a large, well-known Internet project to model protein-folding behavior.

"Computational work can speed a lot of it, but it can't speed all of it. It can maybe speed the first five years," said Pande.

His ongoing "Folding @ Home" project hasn't yet led to a cure for Alzheimer's or other protein-folding diseases, but has generated about 50 scholarly papers and some particularly promising leads, Pande said.

Grid computing is too young to have produced success stories in health care, but "I expect that it will lead to discoveries," said Peter Lyster, a federal specialist in bioinformatics at the National Institute of General Medical Services, a branch of the NIH.

For a computer user, getting involved starts with going to a Web site for any of the dozens of different grid computing projects and downloading a small software program.

The programs can run a little like a screensaver, kicking in only when the user is away at lunch or at a meeting. Or they can be configured to work quietly in the background when users are doing something simple, such as word processing, that demands only a fraction of the computer's brainpower.

Such programs send in results and get new problems to solve via the Internet, which might briefly slow down someone with a dial-up connection, said Texas professor Watowich.

As far as security goes, "if they're done properly, they're as safe as anything else," said Matt Bishop, a computer science professor at UC Davis who recently helped investigate vulnerabilities of electronic voting.

Many projects are affiliated with major universities, and a handful, including the dengue-West Nile effort, are hosted by IBM, which says it hires its own security staff to keep things safe.

Source: The Sacramento Bee

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