SARS researchers in China use SGI technologies to search for genomic clues and anti-SARS drugs
Mountain View 20 May 2003Separated by 676 miles, two key research institutes at ground zero of the severe acute respiratory syndrome (SARS) epidemic are conducting breakthrough research into this mysterious disease, using SGI servers to advance their important work. The Beijing Genomics Institute (BGI) is identifying the genomic basis for SARS in its many variations, while the Shanghai Institute of Materia Medica (SIMM) is pursuing an effective pharmaceutical vaccine or cure. Currently, there is no rapid test available to confirm diagnosis of this newly characterised respiratory illness in a timely manner, and there is no known effective treatment or cure.
At SIMM, researchers are engaged in urgent SARS-related drug discovery
research that encompasses:
- Analysing the genomic sequence of the virus thought to cause SARS and identifying important proteins that may be involved in the infection
- Predicting alterations in the identified proteins expected in this mutable virus
- Constructing 3D models of these proteins and performing virtual screenings to discover active compounds with the potential to combat SARS
- Synthesising and screening candidate drugs
- Performing anti-SARS tests
To date, SIMM researchers have created 3D models of several SARS proteins and have already performed several virtual screenings utilising numerous databases of potential drug compounds. The backbone of this research is a 64-processor SGI Origin 3800 supercomputer, an additional four-processor SGI Origin 3200 server and 15 SGI graphics workstations used to model and virtually screen several million structures with the goal of developing a new compound to combat the SARS virus.
The Origin server handles data-intensive virtual screening tasks and the storage of many huge chemical databases, both of which require the shared memory and scalability of the Origin family's OpenGL application programming interface and NUMAflex technologies. To address the SARS virus' characteristic mutation, the supercomputer is being used to map mutation sites and to create data sets pinpointing the structure of mutant proteins. Researchers utilise their SGI graphics workstations to create 3D models of these protein structures and to analyse the virtual screening results in real time.
SIMM, a branch of the Chinese Academy of Sciences, focuses on discovering new drugs and drug candidates through an interdisciplinary mix of such fields as biology, computer science, molecular biology, informatics and computer-aided drug design.
"Our approach to the pressing need for SARS research is high-throughput virtual screening integrated with chemistry and pharmacology", explained Dr. Jiang Hualiang, head of a key SARS research team at SIMM. "We are hoping within the next three months to find strong candidate compounds that may potentially kill the SARS virus. The SGI Origin supercomputer is incredibly
powerful and stable, a must for such tasks as parallel computation, which is critical in reducing screening time. Our SGI workstations provide crucial visualisation capabilities for constructing 3D models."
The esteemed Beijing Genomics Institute, a member of the International Human Genome Project Consortium, best known for its important work in the sequencing of the rice genome, was founded in 1999. BGI researchers are fast at work sequencing 100 isolates of SARS in order to study the multitude of variations of this unusually mutative virus. In addition, diagnostic kits, vaccine and drug solutions are under rapid development.
BGI, the largest non-profit genomics research institute in the Asia Pacific region and the third-largest genomics research centre in the world, relies on two 32-processor SGI Origin 3000 supercomputers, a 5TB SGI TP9100 Fibre Channel storage systems and several Silicon Graphics O2 graphics systems. These technologies are being used for such vital tasks as the modelling of both the genomic basis of SARS and SARS-related protein sequences, along with a variety of intensive computational applications.
"The institute's threefold mission is to sequence genomes of all kinds, particularly agricultural-related genomes, to advance the study of DNA, RNA, protein structures and bio-informatics and to conduct research on human health-related issues, including not only the current SARS initiative but also genotyping and antibody-antigen studies", stated Dr. Wang Jun, who heads the BGI's Beijing campus and its bio-informatics department. "All of these goals present huge high-performance computing demands, especially in the areas of comparative studies and genome-related analysis. Our SGI infrastructure uniquely meets our large and very complex HPC and graphics challenges."
"We are honoured that SIMM and BGI, two world-renowned institutes conducting valuable research into a devastating disease, are using SGI products to accelerate insight and discovery", stated SGI CEO and Chairman Bob Bishop. "Many other advanced laboratories are doing the same, because SGI understands the urgency of leading-edge science and of the breakthrough thinking that is needed to succeed."
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