Fastest supercomputer to model protein-folding dynamics
Although new levels of computer power "will be very important for advancing protein folding and other areas of computational biology, computer power alone, in my opinion, will not be sufficient," Dill nternational Business Machines has model the dynamic process by which a says. "Equally important are model develannounced a $100 million research protein folds from an unfolded state into opment, a better understanding of aqueous solvation, better conformational initiative to build a supercomputer its native three-dimensional structure. that is 500 times more powerful than toIBM estimates that the folding mod- search strategies, faster computational alday's fastest computer. The project has el for a 300-residue protein will encom- gorithms for quantum mechanics, and imsparked particular interest in the biomed- pass more than 1 billion forces acting proved classical force fields." Nevertheical research community because protein over 1 trillion time steps. Even for Blue less, he continues, "for modeling of foldfolding is the initial challenge to which Gene, modeling such a folding process ing and docking to advance to the next the new supercomputer will be devoted. is expected to take about a year of level, I believe substantial computer power will need to be available to those comThe computer, which IBM calls Blue around-the-clock processing. The "protein-folding problem" that munities working on the underpinnings." Gene, will be developed to operate at a IBM understands that "computer powspeed exceeding 1 petaFLOPS (1 x 1015 chemists, biochemists, and biologists are FLOPS). FLOPS means floating-point op- trying to solve actually has two parts. er alone will not be enough to solve such eration per second, and a floating-point "One is to gain a microscopically detailed an incredibly complex and fundamental operation is a basic arithmetic operation understanding of a protein's dynamics problem" as protein folding, replies IBM such as an addition or multiplication step. as it repeatedly crosses the barrier from Media Relations Manager Charles E. Jenkins Jr. "In addition to the A petaFLOPS computer | computer-architecture exwould be 40 times faster ^ ^ " ^ — 's perts building the Blue Gene than the combined power of Blue Gene will model the detailed folding I computer, scientists with the 40 quickest supercomdynamics of proteins like barnase o IBM's Computational Bioloputers in the world today, gy Center will be working on would have 1,000 times the understanding the fundaperformance of IBM's Deep mentals of protein folding," Blue computer (which beat he notes. world chess champion Garry Kasparov in 1997), and Chemistry professor Euwould be about 2 million gene I. Shakhnovich of Hartimes more powerful than a vard University, whose retypical desktop personal Folded search interests include thecomputer. According to oretical and experimental IBM, the two fastest comprotein folding, says IBM's puters in the world today, part of the De- the unfolded ensemble to the native initiative "is potentially a very useful and partment of Energy's nuclear weapons form and back again," says biophysics powerful approach that will give resimulation program, have a performance and biophysical chemistry professor searchers in the field a very important of about 2 teraFLOPS (2 x 1012 FLOPS) George D. Rose of Johns Hopkins Uni- tool to approach the protein-folding probeach, less than 0.2% of Blue Gene's antici- versity School of Medicine, who special- lem. Currently, very detailed models that pated speed. izes in protein folding and structure. include all protein atoms can be folded From a hardware standpoint, Blue "The second is to develop simple guid- using special force fields." But the new Gene will have more than a million 1-giga- ing principles" for predicting structure supercomputer will make it feasible to FLOPS processors. But it will occupy less from sequence. "In my opinion, fast model protein folding with more realistic than 2,000 sq ft of space, about the same computers are important for the former, force fields using their natural sequences, Shakhnovich says. but much less so for the latter." amount as a small single-family home. IBM believes the supercomputer will The choice of protein folding as an iniNevertheless, he adds, "I think developbe ready to go in aboutfiveyears. The de- ment of a petaFLOPS machine is consis- tial project for Blue Gene shows that the sign concept for the machine is called tent with our national scientific priorities." "era of the protein is here and recogSMASH (simple, many, and self-healing) Regardless of IBM's specific reasons for nized," comments biophysics professor because it involves use of a simplified set developing it, "all of the unintended con- Charles L. Brooks III of Scripps Research of processor instructions, a massively sequences are likely to be very good." Institute, La Jolla, Calif., who specializes parallel architecture with 8 million simulPharmaceutical chemistry professor in the theory of protein folding and the taneous threads of computation (com- Ken A Dill of the University of California, application of computational statistical pared to a maximum of 5,000 in current San Francisco, whose research also fo- mechanics to the study of protein folding. computers), and an automated ability to cuses on protein folding, says the level of Blue Gene will likely result in more comovercome failures in processing compo- computer power IBM is planning "will be putational "experiments" being run and nents and computing threads. terrific, for two reasons: for what this sin- more ideas being tested per unit time, he The supercomputer will initially be gular onslaught may accomplish on its says, "and this will lead to rapid increused to model the folding of a human own and for the new technologies that mental improvements in our understandprotein of average size—about 300 ami- may trickle down into machines that are ing of protein folding." no acids long. IBM researchers aim to accessible to a broader community." Stu Borman
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DECEMBER 20,1999 C&EN 3 5
