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Joint Center for Molecular Modeling Instituted by Burnham Institute for Medical Research & UC San Diego

A group of researchers led by Dr. Adam Godzik at the Burnham Institute for Medical Research is creating tools to speed up the understanding of information gathered// from the human genome project. Rich with $2.1 million funding available to them over a three year period, this consortium, under the name Joint Center for Molecular Modeling, will seek to provide adequate support to scientists from Burnham and UCSD's Computer Science and Engineering department as they team up to develop innovative software.

Researchers are sequencing millions of genes per year in different genomic projects. Solving the structures of the protein products of these genes proceeds at a slower pace of between 3,000 and 5,000 per year. Using the structures of proteins that have already been solved, Dr. Godzik and co-principal investigators Drs. Pavel Pevzner, Yuzhen Ye and Piotr Cieplak will develop novel ways to extract rules and trends of how structures change and evolve. They will use these tools to predict how, for instance, a human protein would differ from its counterpart in mice or bacteria.

"Protein structures can be solved experimentally in a couple of months, sometimes weeks," said Dr. Godzik. "Scientists around the world have already solved tens of thousands of them. Structures of many proteins can also be predicted on a computer in a matter of minutes, but the quality of such models is generally so poor that they are not useful in many applications, such as drug design. We have developed tools that allow us to learn from structures already solved and apply that knowledge to improve predicted structures of new proteins. This funding from the National Institutes of Health makes it possible for us to prove our concept and make our tools available to scientists worldwide."

"Dr. Godzik brings together an interdisciplinary team with an impressive track record," said Dr. Jerry Li, Program Director of the National Institute of General Medical Sciences a t the National Institutes of Health, which funded the new project. "By developing and using new computational approaches, the group will improve our ability to accurately model the three-dimensional structures of proteins, which are invaluable to functional studies and rational drug design."

Adam Godzik, Ph.D., is Professor and Director of the Bioinformatics and Systems Biology Program at the Burnham Institute for Medical Research. Yuzhen Ye, Ph.D., and Piotr Cieplak, Ph.D., are Research Assistant Professor and Staff Scientist, respectively, at the Burnham. Pavel Pevzner, Ph.D., is the Ronald R. Taylor Professor of Computer Science in the Department of Computer Science and Engineering at UCSD's Jacobs School of Engineering.

According to Pevzner, predicting protein structures represents a rich source of new algorithmic challenges. "In recent years new mathematical tools have revolutionized the way we describe rearrangements of genomic elements and domain reshuffling in multi-domain proteins," said Pevzner. "We believe that they can also be used to recognize and describe the movements of micro-domains in protein structures, and that will be the focus of the Computer Science and Engineering department's participation in this collaboration with the Burnham Institute."

Source :Eureka Alert


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