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Generally obtained by X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy, the data is released into the public domain and can be accessed for free. It currently has more than 44,000 proteins.
"Drug design is done in different ways, he says. "Historically it has been done using the technique of high-throughput screening and robotics. Thousands of compounds are tested experimentally to see if any will show activity [potency] against a given disease, for example, something like Ebola or SARS. Computational drug design is a more focused approach. A specific protein implicated in the disease is identified and then drugs are designed to target [bind with] only that specific protein. Part of that is using visualization in computer modeling and X-ray crystallography."
A key element in Stony Brook's research comes from NVIDIA Software (Santa Clara, Calif.) and its Quadro family of GPUs. Three-D graphics have been used for many years to allow researchers to visually evaluate molecule surfaces.
Special glasses that fool the eye into seeing sharper, more realistic depth and dimension have been commercially available for some time, but were originally supported only on expensive, proprietary high-performance graphics systems. The cost restricted the number of research stations available at Stony Brook.
"The way we use NVIDIA is that we have a desktop PC," Rizzo says. "In that we have the NVIDIA graphics card and plug it into a three-pin connector to an infrared emitter [from StereoGraphics]. It emits pulses. We wear infrared glasses and stereo glasses from StereoGraphics or NuVision. Given all that, we can visualize the protein and drug model in 3D, given the right software.