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"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."