Institute for Systems Biology Symposium addresses need for better computational tools such as World Community Grid

Seattle 25 April 2005The Institute for Systems Biology (ISB) announced at its 2005 international symposium on Computational Challenges in Systems Biology that ISB's Human Proteome Folding Project launched on IBM's World Community Grid in November 2004 has already predicted 50.000 protein structures. The project, funded by IBM and tapping into the unused computational power of idle computers is helping predict the shape of human proteins and helping make new scientific and medical breakthroughs come at an ever faster pace - certainly more rapidly than in any new field of biology in the 20th Century. Annotating these proteins of unknown function remains a critical bottleneck for systems biology and is crucial to understanding the biological relevance of genome-wide changes in mRNA and protein expression, protein-protein and protein-DNA interactions.


"This project showcases the enormous power of collaborations", stated Dr. Richard Bonneau, senior scientist at the Institute for Systems Biology. "Through a partnership with IBM we are utilizing World Community Grid which is enabling us to complete a project in less than a year that would have taken us approximately 100.000 years to complete with the current computational power at ISB. We have already predicted 50.000 protein structures and are well on our way to reaching the goal of between 100.000-150.000 structures."

World Community Grid is enabling ISB researchers to predict three-dimensional structures, which are more highly conserved than one-dimensional structures. Understanding three-dimensional structures allow researchers to identify the presumptive function of proteins. These functions can then be assigned to appropriate networks. Researchers expect that approximately 2/3 of the folded proteins will result in correct topologies and that approximately 1/3 of the predicted structures will match previous folds now stored in the protein data bank/PDB.

Folded proteins explain many biological functions - just as the parts in a car determine the role they play in the car's function, three-dimensional protein structures of protein determine the roles they play in living organisms. Once completed, the Human Proteome Folding Project will enable ISB to provide a new proteomics tool that can be widely used by the academic community in an open source environment.

Speakers at this year's symposium included Rich Bonneau, ISB senior scientist and Viktors Berstis, Senior Software Engineer at IBM Global Services, outlining current efforts to run Rosetta de novo structure prediction on World Community Grid, and applications of this new dataset to the re-annotation of proteins of unknown function in over 60 complete genomes via de novo structure prediction. Other presenters included keynote speaker Dr. Nathan Myhrvold, Founder of Intellectual Ventures LLC and former chief technologist at Microsoft Corporation who founded Microsoft Research, and world leaders in the area of computational biology.

The Institute for Systems Biology (ISB) is an internationally renowned non-profit research institute dedicated to the study and application of systems biology. ISB's goal is to unravel the mysteries of human biology and identify strategies for predicting and preventing diseases such as cancer, diabetes and AIDS. The driving force behind the innovative "systems" approach is the integration of biology, computation, and technology. This approach allows scientists to analyse all of the elements in a system rather than one gene or protein at a time. Located in Seattle, Washington, the Institute has grown to 11 faculty and more than 170 staff members; an annual budget of more than $25 million; and an extensive network of academic and industrial partners.

To date, more than 100.000 computers are participating in World Community Grid but more are needed to continue this important work. Individuals can volunteer their computer's idle computing time by joining at World Community Grid is powered by IBM technology, which includes IBM eServer p630 and x345 systems and IBM's Shark Enterprise Storage Server running IBM DB2 database software and the AIX and Linux operating systems.

IBM DB2 software will support millions of SQL queries a day as it manages all aspects of the data provided by potentially millions of computers working in concert. World Community Grid will harnesses computing time donated by potentially millions of PCs and laptops around the world for humanitarian research. More news about ISB and the World Community Grid is available in the VMW December 2004 article Institute for Systems Biology to fold human proteome on World Community Grid.

Leslie Versweyveld

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