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

"Stereo optics devices provide extra dimension and clarityŚwe can see much more clearly the interactions between a potential drug compound and a target protein molecule. While this capability used to be very expensive and only available to select researchers, Quadro makes it affordable."

One of the keys is how the drugs dock, or react to each other. The NVIDIA GPU takes some of the mathematical tedium out of the process, says Jeff Brown, general manager, NVIDIA Professional Solutions. "There's a lot of math going on there in all the simulations. Huge variables are being done on the fly. What you see is the result of that math, called rendering. These are physics calculations that super computers used to do. Now clusters of graphics processors can do a lot more iterations. They're providing the tools that scientists need. It helps them move applications and optimize them on GPUs."

In docking, molecular modeling techniques are used to predict how macromolecules (typically proteins) interact with other molecules, which may be other proteins, nucleic acids or small drug-like molecules. How a protein interacts with small molecules may enhance or inhibit its biological function. This plays an important role in the rational design of drugs.

"The idea," Rizzo says, "is that drugs fit a target like a lock and key. If you understand the interactions of drug and protein, your brain is the best computer. It picks up things during the analysis. With docking, you can look for a new drug for any given target using computation. You dock in the molecules one at a time and compute its binding properties.

Computation, in various forms, speeds up the drug discovery process which of course is vitally important."



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