Advanced Imaging

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Advanced Imaging Magazine

Updated: January 12th, 2011 10:01 AM CDT

Speeding Up Drug Discovery with Imaging

A picture is worth a thousand math calculations
Compounds are evaluated for compatibility with a binding site in HIVgp41 using NVIDIA Quadro stereo graphics
© Robert C. Rizzo, Stony Brook University
Compounds are evaluated for compatibility with a binding site in HIVgp41 using NVIDIA Quadro stereo graphics. This figure was generated using Molecular Operating Environment (MOE) from Chemical Computing Group.
Setup for a computational virtual screening
© Robert C. Rizzo, Stony Brook University
Setup for a computational virtual screening (docking) experiment aimed at discovery of new compounds (green) that inhibit a target protein (gray) from influenza. This figure was generated using UCSF Chimera interactive molecular visualization and analysis system.
NVIDIA's Quadro system
"With a simple PC and a video card, I can virtually step inside a complex molecule and find the best docking sites for potential drug compounds," Stony Brook University's Robert Rizzo says of NVIDIA's Quadro system.
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By Barry Hochfelder

Another element the GPU provides is programmable shading technologies. Material properties, set by the scientist, make the molecule easier to view. Color and lighting effects are added that help enhance the image and make more easily recognized.

"You create a particular light and color," NVIDIA's Brown explains. "Things become more intuitive and easier to view. It helps you get away from numbers and to the human eye. The GPU is capable of assigning a huge range of colors and light. The scientists tell the GPU what properties and where the light source is. They're looking for particular surface features—how the molecules move, how strong the bond is, how likely they are to stay together."

As researchers look at the binding between drugs and their target receptor molecules, they can also characterize how mutations that occur in HIV, cancer or influenza affect binding. Stereo visualization allows for a better understanding of what happens at the atomic level, which ultimately enables the creation of new drugs.

"The GPU is a tool for those guys to run the math on and visualize what they're doing," Brown says. "A picture is worth a thousand math calculations."

And yet, the process is not an overnight success. "It still takes 10-12 years and upwards of a billion dollars," says Rizzo. "It's still an incredibly complex and difficult process. The technology does make it easier, but it's not a magic bullet. It's all a collaborative process. Stereo visualization technologies help make it visible and more understandable."



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