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Eyeing US Life Science Market, Japan's NEC Unveils Prototype Molecular Dynamics Appliance

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Tokyo-based IT giant NEC is dipping a cautious toe into the US life science informatics waters with an early version of its Express5800/MD Server, a dedicated appliance for speeding up molecular dynamics simulations.

NEC launched MD Server in Japan in November, but the product is not yet available for sale in the US. While the firm has a strong foothold in the Japanese life science market — it launched its life science division in 1985 — MD Server will mark its first US product, and it's not taking any chances.

The company is currently lining up beta testers to provide feedback on the system, Michael Zeldin, director of bioinformatics at NEC, told BioInform. "We are still talking to experts in the field, we're doing field testing, evaluation, trying to get the kinks out, and trying to make it easier for the user," he said.

NEC unveiled MD Server at Cambridge Healthtech Institute's Structure-Based Drug Design conference in Boston last month [BioInform 06-16-06], where the company also had two posters on virtual screening methods and sheaves of literature on other life science IT products that it markets in Japan.

NEC's life science business encompasses a range of activities targeting preclinical and clinical research, Zeldin said. In addition to the MD Server, the company offers MolStudio/MD, post-processing software for the Amber molecular dynamics package; the Human Kidney Glomerulus Proteome Database, which it developed in collaboration with the Institute of Nephrology at Niigata University; a virtual screening service; and a data-mining service. It has also jointly developed a proteomics data-management software platform called Solphi with Shimadzu. The companies launched that product in October.

NEC has not yet marketed any of these products in the US, but that is likely to change over the next year or so, according to Zeldin. NEC is "aware that healthcare and life sciences are international in character, so what we're interested in doing is identifying those particular solutions that, when they become mature enough and robust enough, would make sense to introduce them to a broader market scope," he said.

Zeldin said that NEC views its image-analysis systems as one example of a technology that has potential in both the preclinical and clinical global market and NEC's MD server can find a place in the pre-clinical market in the US and other markets.

In Japan, MD Server users run PrestoX, a molecular dynamics package developed by Japan's Ministry of Economy, Trade, and Industry. PrestoX readouts are in Japanese, however, so for the US version, the company has ported the Amber package from the University of California, San Francisco, and is considering other popular MD packages like Charmm, developed at Harvard University and marketed by Accelrys.

While hesitant to provide specific benchmarks, Zeldin said that MD Server offers a "theoretical speedup" over a conventional single-node server of "on the order of 100 or more."

But NEC anticipates that the primary benefit of the system will be accuracy, rather than speed. Zeldin noted that because molecular dynamics algorithms are extremely computationally intensive, most methods rely on "cutoffs" that make assumptions about water molecules or omit calculations of interactions between long-distance atoms. While this speeds up the process considerably, "you make a sacrifice in accuracy," Zeldin said, "and as you make sacrifices in accuracy, the value, for example, in drug design and medicinal chemistry goes way down."


"This is an appliance. It does a particular set of calculations. It doesn't do dishes, it doesn't wash clothes. It does a particular job, and that's molecular dynamics."

In addition, he said, even with cutoffs, many calculations can take weeks or months to complete.

MD Server promises to reduce that time without taking any computational shortcuts. The goal for NEC, Zeldin said, is to "achieve sufficient speedup that makes it more cost effective to use the server to gain the accuracy and the speed than it would be to, for example, add processors yourself to your general-purpose computational platform."

The system operates as a standalone appliance, but can also be plugged into an existing computational infrastructure, Zeldin said. He stressed, however, that the MD Server is not designed to replace general-purpose high-performance computing systems. "This is an appliance. It does a particular set of calculations. It doesn't do dishes, it doesn't wash clothes. It does a particular job, and that's molecular dynamics."

US pricing has not yet been determined, but Zeldin said that the target was about $120,000.

The company has not yet set a target launch date for the system, either. "We'd like to go as fast as we can, but not so fast that we overrun what users and people who are interested in this field are looking for, which is dependability, price/performance issues, flexibility of use, ease of inputting, and defining the kinds of problems best addressed by the MD server," Zeldin said.

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