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Institute for Systems Biology Symposium Addresses Need for Better Computational Tools

The Institute for Systems Biology announced today 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.

"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."

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.

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 -- ju st 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 reannotation 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.


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Source:Institute for Systems Biology


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