Pittsburgh Supercomputing Center Will Host Specialized Machine for Biomolecular Research

With stimulus funding from NIH, the National Resource for Biomedical Supercomputing at the Pittsburgh Supercomputing Center will soon be accepting proposals for biomedical researchers to use a novel special-purpose supercomputer for biomolecular simulation that is being made available without cost by D. E. Shaw Research.

PITTSBURGH, PA., May 5, 2010 – The National Institute of General Medical Sciences (NIGMS), part of the National Institutes of Health (NIH), has awarded a two-year, $2.7 million grant to the National Resource for Biomedical Supercomputing (NRBSC) at the Pittsburgh Supercomputing Center (PSC) to host a specialized supercomputer for biomolecular simulation designed by D. E. Shaw Research (DESRES). The machine, called Anton, will be made available without cost by DESRES for non-commercial research use by universities and other not-for-profit institutions.

Anton was designed to dramatically increase the speed of molecular dynamics (MD) simulations compared with the previous state of the art, allowing biomedical researchers to understand the motions and interactions of proteins and other biologically important molecules over much longer time periods than have previously been accessible to computational study. The machine and the novel algorithms it employs were designed by a team of researchers led by David E. Shaw, chief scientist of DESRES.

NRBSC will soon be inviting U.S. biomedical researchers to submit proposals for allocations of time on the Anton machine. A peer review committee to be convened by the National Research Council will review proposals. Although the NIH has supported MD-related research by individual scientists for many years, it has never before provided funds to make a supercomputing system for MD simulations available as a national resource. For more information about proposal submission, see: http://www.nrbsc.org/anton_rfp

“This is an incredibly exciting project in many ways,” said Joel Stiles, the director of NRBSC. “With this very generous gift from D. E. Shaw Research and the funding provided by NIH, we are deploying a tool of unprecedented power for the benefit of biomedical researchers nationally. We hope and expect that this project will help to significantly advance our understanding of biomolecular structure and function, and to spur ongoing scientific and technological development in MD research and in other areas of computational biology.”

As part of the NIGMS award, NRBSC also will install a new data storage and analysis subsystem, including nearly half a petabyte of online disk capacity (one petabyte is one million gigabytes), to host and make widely available the tremendous amount of data that will be produced by MD simulations on Anton. In addition, Stiles, a faculty member in Biological Sciences and the Lane Center for Computational Biology at Carnegie Mellon University, is collaborating with Christopher Langmead in the Carnegie Mellon School of Computer Science to develop specialized software for the analysis of data as it streams off the machine.

While experimental methods such as X-ray crystallography can determine rigid molecular structures at near atomic resolution, MD simulations track atomic positions over the course of time. Changes in the shape of a biomolecule are often intimately related to its function, suggesting that atomic-level molecular dynamics simulations may ultimately play an important role in the design of therapeutic drugs. Because atomic-level MD simulations of proteins require an enormous number of calculations to simulate even a very short period of biological time, many of the most important biological phenomena have historically fallen outside the reach of even the most powerful general-purpose scientific supercomputers. Anton has now run simulations extending for more than a millisecond of biological time, about 100 times longer than the longest previously published all-atom MD simulation.

D. E. Shaw Research is an independent research laboratory that conducts basic scientific research in the field of computational biology. At present, the lab is involved primarily in the design of novel algorithms and machine architectures for high-speed molecular dynamics simulations of proteins and other biological macromolecules, and in the application of such simulations to basic research in structural biology and biochemistry and to the process of computer-aided drug design.

Established in 1987 as part of PSC, with support from NIH’s National Center for Research Resources, NRBSC was the first external biomedical supercomputing program funded by NIH. NRBSC scientists conduct basic research in areas spanning molecular and cellular modeling, massive 3D reconstruction of biological tissues, and bioinformatics. In addition, NRBSC fosters exchange among experts in computational science and biomedicine, provides computational resources and training to biomedical researchers, and provides state-of-the-art educational outreach to students at all levels across the nation.