Institute for Systems Biology to fold human proteome on World Community Grid

Seattle 16 November 2004The Institute for Systems Biology (ISB) in partnership with IBM, United Devices and the University of Washington, has launched the Human Proteome Folding Project on World Community Grid. This project, the first to run on the Grid will help predict the shape of human proteins and further efforts toward predictive, preventive and personalized medicine.

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IBM has selected United Devices' Grid MP software to power the IBM World Community Grid, a volunteer-based distributed computing network for enabling massive-scale, public interest research projects. The inaugural World Community Grid project, called the Human Proteome Folding Project, will harness the power of Grid computing to predict the structure of the 30.000 plus proteins found in the human genome. Currently, the structures of only a fraction of these proteins are known. A protein's shape determines its function, and scientists say understanding protein functions is essential to the successful development of therapeutics to treat illness and disease.

Proteins could be said to be the most important molecules in living beings. Leveraging the computational power of millions of computers, scientists will predict the shape of human proteins that researchers currently know little about. From these predicted shapes scientists hope to learn about the function of these proteins, as the shape of proteins is inherently related to how they function in our bodies. Researchers hope that in doing so we will better understand the causes and potential cures for diseases like cancer, AIDs and tuberculosis.

"Never before has a project of this size taken place using Grid computing technology", stated Ed Hubbard, United Devices president and founder. "Having two massive Grids, capable of performing years of research in mere hours, working together to define all unknown protein structures within the human genome is a huge step forward in the battle against life-threatening diseases. We're proud that IBM selected United Devices to build their own global Grid for enabling these types of critical health research projects."

Systems biology requires the integration of cutting edge biology, technology, computation and medicine. World Community Grid, sponsored by IBM, will enable ISB's researchers to process unprecedented quantities of data, thus furthering its efforts in studying and applying systems biology to the fundamental challenges in biology and medicine. The volume of calculations the ISB will perform on the Grid is large enough to classify this as one of the largest ever. This project would not be possible without a resource like World Community Grid and Grid.org.

"This partnership with IBM provides us with tremendous computational capacity that we would not otherwise have", stated Dr. Leroy Hood, president of the Institute for Systems Biology (ISB). "The Human Proteome Folding Project will help us to better understand a significant fraction of the proteins in the human proteome. Understanding the function of these mystery proteins is critical in our quest toward the predictive, preventive and personalized medicine of the future."

"This project is one of the next logical steps in a progression of events starting with the sequencing of the Human Genome", stated Dr. Richard Bonneau, senior scientist at ISB. "The data gained from this project will facilitate the research and development of health care and life sciences companies across the world seeking to offer breakthrough therapeutics to the public. Now that the Human Genome has been sequenced, the next critical phase in genomics research is to do as much as we can to understand protein functions. This database of protein structures and possible functions will let us take those next steps in understanding how diseases that involve these proteins work."

"United Devices and its Grid MP technology provide a proven, reliable and secure platform for the World Community Grid", stated Stanley Litow, vice president, Corporate Community Relations and president, IBM International Foundation. "We welcome United Devices' participation and expertise as we join together in this global effort to harness the collective computing power of up to six million PCs."

The Human Proteome project running on World Community Grid will split the problem of folding the Human proteome into millions of smaller problems called "work units". Each volunteer will download a small programme that will then periodically contact the central server to get its next work unit.

Utilizing unused CPU, these computers running the Grid client will attempt to fold a single protein from the set of human proteins with no known shape; it will take several "work units" to fold a single protein and there are many proteins being folded. Each computer will try millions of shapes and return to the central server the best shapes found throughout the simulation. As the computers try to fold the protein chains in different ways, they will attempt to find the particular folding/shape that is closest to how the proteins really fold in our bodies.

Just about everything in the human body involves or is made out of proteins. Proteins are actually long chains made up of smaller molecules called amino acids. There are 20 different amino acids that make up all proteins. One can think of the amino acids as being beads of 20 different colours. Sometimes, hundreds of them make up one protein. Proteins typically don't stay as long chains however. As soon as the chain of amino acids is built, the chain folds and tangles up into a more compact mass, ending up in a particular shape. This process is called protein folding.

Protein folding occurs because the various amino acids like to stick to each other following certain rules. One can think of the amino-acid - beads on a string - as being sticky, but sticky in such a way that only certain colours can stick to certain other colours. The amino acid chains built in the body must fold up in a particular way to make useful proteins. The cell has mechanisms to help the proteins fold properly and mechanism to get rid of improperly folded proteins. Each gene tells the order of the amino acids for one protein. The gene itself is a section of long chain called DNA.

In recent years scientists sequenced the human genome; finding over 30.000 genes within the human genome. The collection of all human genes is known as "the human genome". Depending on how genes are counted, there are more than 30.000 genes in the human genome. Each of these genes tells how to build the chain of amino acids for each of the 30.000 proteins. The collection of all of the human proteins is known as "the human proteome".

What the genes don't tell is how the proteins will fold into their compact final form. The final shape of a protein determines its function, and its ability to connect or interact with other proteins, and as a result, is critically important. For example, muscle proteins connect to each other to form a muscle fiber. Proteins stick together in a particular way because of their shape, and certain other factors relating to their shape.

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 seven faculty and more than 170 staff members; an annual budget of more than $25 million; and an extensive network of academic and industrial partners.

United Devices' Grid MP technology enables organisations to harness the power of on-line computers to enable computational research and analysis projects on a massive scale. Previous United Devices Grid projects have powered public cancer, anthrax and smallpox research projects. The technology is also revolutionizing research and development and business processing at top pharmaceutical companies like Novartis and Johnson & Johnson.

Leveraging the unparalleled power of Grid computing, it is anticipated that the project will reduce an estimated 300.000 years of conventional computational time to less than 12 months. However, according to scientists at ISB, it will take years before the research leads to new vaccines or biotechnology applications. Once the project is complete, IBM's World Community Grid and United Devices' grid.org will operate as separate entities running their own individual research projects.

Volunteers wishing to participate in the Human Proteome Folding Project can visit the IBM Grid to download software that runs research-related data during PC downtime. The programme is secure and unobtrusive, and uses Grid MP technology to pass data and results from the user's PC to IBM's data centre.

United Devices is specialized in enterprise Grid solutions. The company's Grid MP platform is used to operate clusters of any size as well as aggregate compute resources on a network to create an enterprise Grid capable of running a wide range of high-performance computing applications in life sciences, geosciences, manufacturing, financial services, chemical engineering and other industries. The company's solutions are available in both enterprise and on-demand deployments. United Devices also operates the world's largest Grid for grand-scale research that consists of almost three million desktop, portable and server systems in more than 220 countries.

The project will run concurrently on United Devices' http://www.grid.org, the world's largest computational Grid dedicated to life science research. More news on United Devices is available in the VMW February 2004 article United Devices' Global Grid surpasses 2,5 million connected devices in fight against cancer and smallpox.


Leslie Versweyveld

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