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Computing for a Cure

One We'd Like to End

  • June 21, 2006
  • By Drew Robb

Silver anniversaries are normally joyous occasions, but not this one. June 5, 2005 marked the 25th anniversary of the discovery of AIDS. Amid the calls for greater awareness and increased funding was recognition that, from a medical viewpoint, billions of dollars spent on research had produced little progress in recent years.

This may soon change. Researchers at the State University of New York's (SUNY's) campus at Stony Brook are using a new SGI supercomputer to model the behavior of the molecules that lead to the creation of the human immunodeficiency virus (HIV). Although the structure of these molecules has been known for more than 10 years, experiments could not determine how the drugs get in and out of them. These simulations fill in the missing piece and will open the door to creating drugs that block the virus' activities.

"People have tried to create simulations of this before but weren't able to," says Dr. Carlos Simmerling, associate professor at SUNY Stony Brook's Center for Structural Biology. "The convergence of a lot of technologies that have been developed brought us to the point where we thought it would be a good time to try to solve this problem."

To create the simulation, SUNY Stony Brook uses an SGI Altix system with 1024 Intel Itanium 2 processors. It runs on Linux and has 3 TB of memory.

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