SYSTEMS

The Institute for Systems Biology (ISB) announced today that in partnership with IBM, United Devices and the University of Washington, it 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. 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. "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," stated Dr. Rich Bonneau, ISB lead scientist on the project. "This database of protein structures and possible functions will let us take those next steps in understanding how diseases that involve these proteins work." 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. "We are truly excited to partner with IBM on this project," stated Dr. Leroy Hood, ISB president. "I applaud IBM for its visionary approach in establishing World Community Grid and am convinced that the enormous computational power they are providing in cooperation with United Devices will lead to unprecedented results in our ability to understand this next critical phase in genomics research." 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 (sign up by going to worldcommunitygrid.org) will download a small program that will then periodically contact the central server to get its next work unit. "World Community Grid represents a new model for philanthropic giving," said Linda Sanford, IBM senior vice president of Enterprise On Demand Transformation and Information Technology and head of the World Community Grid Advisory Board. "IBM is involved in World Community Grid because just as we do for clients, we're committed to bringing the best technologies forward to address critical societal and health issues. World Community Grid demonstrates that government, business, and society can be the direct beneficiary of innovation if we are willing to rethink the way innovation and science both develop and prosper." 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 colors. 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 colors can stick to certain other colors. 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. Background: 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 analyze 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. For more information about the ISB or the Human Proteome Folding Project, visit: www.systemsbiology.org 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 harness computing time donated by millions of PCs and laptops around the world for humanitarian research. For more information about the Human Proteome Folding Project, visit worldcommunitygrid.org