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IBM to Undertake Protein Folding Analysis with New Supercomputer, Blue Gene

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NEW YORK--IBM last month announced that a super-computer it is designing to be capable of one quadrillion operations per second will be used initially to tackle the "grand challenge" of modeling the folding of human proteins. The company and its life science industry and academic partners will deploy the $100 million RS/6000 machine, called Blue Gene, to create three-dimensional models that show how proteins fold. IBM Research announced later in the month that it would complement the initiative by awarding, in coordination with the Protein Structure Initiative of the US National Institute of General Medical Sciences, grants of up to $1 million for the purchase of IBM supercomputing technology to research centers working in the field of structural genomics.

To test its Blue Gene technology, IBM will begin soon to fold a set of small proteins with 30 or 40 amino acids each, according to Paul Horn, senior vice-president of IBM’s research division. Then, in four years when the computer is completely constructed, a much larger protein will be selected for a year-long project during which Blue Gene will be run 24-hours a day, 7 days a week.

Horn predicted that most of the protein folding data it generates will be made available to the scientific research community at large, but that access to certain findings could be allowed exclusively to IBM’s life science industry partners who include Aventis, Bristol-Myers Squibb, and Merck.

IBM said it expects construction of the one-million-processor supercomputer, which is being conducted at IBM’s Watson Research Center in Yorktown Heights, NY, to take four to five years. Blue Gene will be 1,000 times more powerful than IBM’s Deep Blue machine and 500 times faster than today’s most powerful supercomputer, IBM claimed.

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