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"3D CRUNCH" COMPUTING CHALLENGE TO IMPACT

DRUG DISCOVERY

 

Silicon Graphics Teaming With Glaxo Wellcome, Imperial Cancer Research Fund,

The Swiss Institute of Bioinformatics and the Lyon Bioinformatics Center

to Predict Thousands of New Protein Structures

 

CORTAILLOD, SWITZERLAND (May 18, 1998) — Silicon Graphics, Inc. (NYSE:SGI) today announced that it is working with leading international bioinformatics research organizations in a major scientific and technological undertaking called "3D Crunch." The project, launched today, will analyze over 200,000 public protein sequences and use advanced technology to predict 50,000 new 3D protein structures. Its findings will be accessible via the World Wide Web, expanding scientists’ knowledge of proteins and ultimately accelerating drug discovery to combat disease.

 

A Silicon Graphics® CRAY® Origin2000TM server will serve as the computing engine for 3D Crunch. The software component of the project will be spearheaded by bioinformatics and protein modeling experts from Glaxo Wellcome, the Imperial Cancer Research Fund (ICRF), The Swiss Institute of Bioinformatics (SIB) and the Lyon Bioinformatics Center (PBIL) at the University Claude Bernard.

 

Scientists study proteins and their structures using bioinformatics and protein modeling methods to improve their understanding of disease processes. By identifying how proteins function in humans, viruses or bacteria, and the roles proteins play in disease, scientists can design drugs to interfere with or enhance specific protein activity in order to cure or prevent disease. Key to this understanding is the structure, or 3D shape, of a protein, which helps determine its function. The combination of high-performance computing combined with advanced analysis algorithms and applications supplements laboratory methods, providing cost and time savings to drug research.

 

Located at the Silicon Graphics European Advanced Technology Center in Cortaillod, Switzerland, the 64-processor CRAY Origin2000 server will power SWISS-MODEL, the 3D protein modeling software developed by Dr. Manuel Peitsch, worldwide director of scientific computing at Glaxo Wellcome and his research team. The SWISS-MODEL program will analyze the 200,000 public protein sequences in the SWISS-PROT* and TrEMBL* databases, and predict their 3D structures by comparing them to related proteins with known structures stored in the Protein Databank (PDB)*. Then, for those sequences that cannot be predicted by SWISS-MODEL, additional analysis with software and databases developed at the ICRF and the PBIL will be performed. The program FOLDFIT, developed jointly by the ICRF and Glaxo Wellcome, will be used to suggest a function for the bacterial protein sequences in the databases that cannot be modeled with comparative methods such as SWISS-MODEL.

 

"Silicon Graphics works closely with innovative researchers who are applying new technologies to solve complex problems with human-life impact," said John R. "Beau" Vrolyk, senior vice president of the Server and Supercomputing Business Unit for Silicon Graphics. "The benefits to the healthcare industry as a result of improvements in data management and analysis technologies will be seen in the increase in the number of options and quality of healthcare products available to the medical consumer."

 

"Today, most of the 4,500 protein structures available to the world have been generated by the difficult and time-consuming work required in traditional laboratory methods," said Dr. Peitsch. "We’re compressing essentially a year of computing time down to a week, thanks to the power of the CRAY Origin2000 server. 3D Crunch will provide a significantly larger resource of computationally-generated structural information to researchers throughout the global scientific community, profoundly advancing our ability to understand the function and structure of proteins important in drug discovery and design."

 

"This exciting project uses highly sophisticated computer hardware and software to extract novel structural and functional information from the rapidly increasing volume of gene sequence data," said Dr. Paul Nurse, director of the Imperial Cancer Research Fund in London. "These studies can give us valuable insights into the molecular basis of human diseases such as cancer."

 

Silicon Graphics has participated in similar milestone computing projects dedicated to expanding scientific knowledge to improve drug discovery. In 1996, Silicon Graphics, the European Molecular Biology Laboratory (EMBL) and the European Bioinformatics Institute (EBI) demonstrated the power of computing by conducting a genome analysis project called "GeneCrunch" live on the Web. Another computing challenge, "SpaceCrunch," sponsored by Silicon Graphics and Tripos, Inc. took place in 1996 and enabled scientists to search the largest virtual combinatorial chemistry database over the Web.

 

3D Crunch will last for approximately a week. Scientists will then compile and make the resulting database publicly available through the project participants’ Web sites.

 

OriginTM servers are based on breakthrough CC-NUMA (cache-coherent Non-Uniform Memory Access) technology which provides unmatched high-performance computing and scalability through its interconnect technology.

 

3D Crunch Web Sites:

Silicon Graphics: http://www.sgi.com/chembio

SWISS-MODEL: http://www.expasy.org/swissmod/

Glaxo Wellcome: http://www.glaxowellcome.co.uk.

ICRF: http://www.icnet.uk/bmm

SIB: http://www.expasy.org/

PBIL: http://pbil.univ-lyon1.fr

 

Additional Reference Sites:

PDB: http://www.pdb.bnl.gov/

SWISS-PROT: http://www.expasy.org/sprot/ (links to TrEMBL included)

EBI (TrEMBL database): http://www.ebi.ac.uk

 

* The SWISS-PROT and TrEMBL databases are developed jointly by the group of Amos Bairoch at the newly created Swiss Institute of Bioinformatics (SIB) and the group of Rolf Apweiler at the EMBL outstation - the European Bioinformatics Institute (EBI).

 

* PDB (http://www.pdb.bnl.gov) was established at Brookhaven National

Laboratory, New York, in 1971 and has been developed by the Protein Data

Bank team over the past 26 years - with now 11 mirror sites throughout

the world. Joel L. Sussman is Head of the PDB.

 

Silicon Graphics, Inc. is a leading supplier of high-performance interactive computing systems. The company offers the broadest range of products in the industry — from low-end desktop workstations to servers and high-end Cray® supercomputers. The company’s key markets include the manufacturing, government, sciences, communications and entertainment sectors. Silicon Graphics and its subsidiaries have offices throughout the world, worldwide headquarters in Mountain View, California, and European headquarters in Theale, UK.

Silicon Graphics and the Silicon Graphics logo are registered trademarks, and Origin and Origin2000 are trademarks of Silicon Graphics, Inc. Cray is a registered trademark of Cray Research, Inc, a wholly-owned subsidiary of Silicon Graphics, Inc. All other trademarks are the properties of their respective owners.

 

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