ACADEMIA

MOUNTAIN VIEW, CA -- SGI® (NYSE: SGI) supercomputing solutions installed in January 2002 are now helping users at the Buffalo Center of Excellence in Bioinformatics to conduct important research in structural biology that will affect such crucial areas as the development of more effective antibiotics. The 64-processor SGI® Origin® 3800 server is being used by a team including Dr. Russ Miller, director of the University at Buffalo's (UB) Center for Computational Research (CCR) and UB distinguished professor in the Department of Computer Science and Engineering; Dr. Charles M. Weeks, senior scientist at the Hauptman-Woodward Medical Research Institute (HWI); and Nobel Laureate Dr. Herbert A. Hauptman, president of HWI and UB Distinguished Professor in the Department of Structural Biology in the UB School of Medicine and Biomedical Sciences. Their research objective is to determine and refine the structure of proteins through the enhancement of SnB, the protein-structure software of choice that was developed by the UB/HWI team and is now used by more than 500 drug-design and research labs. SnB, based on the Shake-and-Bake algorithm developed by Hauptman, has become a critical tool for determining the structures of biomedically important molecules-including vancomycin, known as the antibiotic of last resort. One goal of the team's efforts with vancomycin has been to ensure the effectiveness of this drug against pathogens that cause serious blood and respiratory infections. SnB is expected to gain even wider use now that the human genome has been sequenced. The UB/HWI team now is pursuing collaborations with other researchers that will allow the determination of much larger proteins, the work at the heart of the emerging field of proteomics. The Shake-and-Bake algorithm for molecular structure determination is listed as one of the top 10 algorithms of the 20th century by IEEE Computing in Science & Engineering. "My first attempt at using Shake-and-Bake on an earlier Origin system reduced the time to determine the molecular structure under consideration from hours to just seconds," said Dr. Miller. "The computational power and ease of use of SGI technology served as a platform from which to attack significantly larger molecular structures than we had previously considered. "Not surprisingly, we expect to understand the interaction drugs have with bacteria more quickly when we apply Shake-and-Bake on the new Origin 3800 server. This will enable scientists to design and modify antibiotics to ensure their effectiveness against emerging strains of disease." In addition to such chemical structure analysis, the Buffalo Center of Excellence in Bioinformatics is using the Origin 3800 server to perform cost-effective, production-quality research in the life sciences, including bioinformatics. For these tasks, scientists at UB are using the SGI high-throughput computing environment for bioinformatics, featuring optimized versions of such standard applications as BLAST, FASTA(TM), Clustal W and HMMER on SGI servers. Through its Visual Area Networking concept, SGI will enable the Buffalo Center of Excellence in Bioinformatics to extend its visualization capabilities to partner institutions and researchers using a recently acquired SGI® Onyx® 300 visualization system. By serving high-resolution output to end users utilizing multiple workstations provided by many vendors, Visual Area Networking technologies extend the capabilities of the new Onyx 300 system, as well as the center's initial 6-CPU Silicon Graphics® Onyx2® visualization system, which has been used by the center for three years for collaborative visualization of chemical models. "The Buffalo Center of Excellence in Bioinformatics is envisioned as a world-class organization, and, as such, it will be crucial for members to be able to access and collaborate in real time on the graphical representations generated in the CCR, regardless of the location of the scientist and the desktop technology available," Miller explained. "SGI's solution gives us the flexibility to do so in the future, as research projects evolve and as other research and academic institutions join the BCOEB." SGI's Chodi McReynolds, director, industry marketing, sciences, added, "The Buffalo Center of Excellence in Bioinformatics demonstrates how the University at Buffalo is using SGI technology's capabilities to every advantage for more efficient computation and more productive research. For 20 years, SGI has provided leading universities and institutions with the means to visualize and test their research, paving the way for discovery and innovation. The impact and return on investment are clear in CCR's achievements and in the vision for the Buffalo Center of Excellence in Bioinformatics, which can offer its participants computing and visualization resources for even greater and more effective collaboration." The installation of the Origin 3800 server is the latest milestone in a long-standing relationship between SGI and the University at Buffalo's renowned Center for Computational Research, which provides the computational and visualization infrastructure for the Buffalo Center of Excellence in Bioinformatics. The CCR, formed at the University at Buffalo in 1998, conducts research for applications such as molecular structure determination and computer animation. SGI technologies are being used to support work in bioinformatics, computational chemistry, computational fluid dynamics, computational physics, telecommunications and cluster computing, among others. The Buffalo Center of Excellence in Bioinformatics, established just last December, is led by the University at Buffalo, with academic partners Roswell Park Cancer Institute and the Hauptman-Woodward Medical Research Institute. It was created as a research, development, education and economic outreach resource for the information technology, biotechnology and pharmaceuticals industries. For further information about the center, visit www.bioinformatics.buffalo.edu/.