“Proteins are part of a complex social network, and rarely act alone. Protein-protein interactions is the term used to describe when two or more proteins ‘partner-up‘ and bind together to carry out a different biological function. While experimental techniques are used to identify the relationships between one protein and another in its cellular neighborhood, computational simulations are still needed to uncover the more complex web of connections for multiple protein partners.
Neuromuscular disease is a generic term for a group of disorders (more than 200 in all) that impair muscle functioning either directly through muscle damage (muscular dystrophy) or
indirectly damaging nerves. It affects one in 2,000 people. These chronic diseases lead to a decrease in muscle strength, causing serious disabilities in motor functions (moving, breathing etc.). The most well-known is muscular dystrophy. In cases of muscular dystrophy contraction of the muscle leads to disruption of the outer membrane of the muscle cells and eventual weakening and wasting of the muscle. Dystrophin is part of a protein complex that connects the cytoskeleton of a muscle fiber to the tissue framework surrounding each cell through the cell membrane. This complex does not form correctly in muscular dystrophy. (Image courtesy Alessandra Carbone).
Distributed computing power from the World Community Grid (WCG) has recently aided the Help Cure Muscular Dystrophy (HMCD) project in capturing all the possible molecular and atomic connections between 2,280 human proteins. The analyzed proteins include those that are known to mutate and induce different forms of neuromuscular disorders, including Muscular Dystrophy.
HCMD is part of a larger-scale venture, the Decrypthon Molecular Docking Project. This is an alliance between AFM (French Muscular Dystrophy Association), CNRS (French National Center for Scientific Research) and IBM, who are using the World Community Grid resources to help them decipher and map all the functions of interacting proteins found in humans to a worldwide repository of information such as the Research Collaboratory for Structural Bioinformatics (RCSB) protein databank.
The first phase of the HMCD project, completed in June 2007, scrutinized relationships among 168 proteins using molecular docking simulations. The researchers predicted that it would have taken over 14,000 years of computational time on a 2 GHz PC to reveal and rule out all possible docking confirmations for all 168 proteins. However a ‘distributed calculation’ allowed them to considerably reduce the processing time. Over 6,000-8,000 donor machines meant the task took under 26 weeks. However, to test 2,280 proteins on a one-to-one basis for phase II of the project, researchers needed a method to significantly reduce the number of configurations they would have to check. Molecular docking data from analysis of the 168 proteins (known to form 84 complexes) helped them develop a fast docking algorithm to predict potential partners for this large pool of proteins.”
See the full article here.
The World Community Grid is comparable to one of the world’s top 15 supercomputers [ curently at 590.673 TeraFLOPS]. Its software has been downloaded onto over two million computers, which together have completed almost 700,000 years of scientific computation.”
World Community Grid (WCG) runs on BOINC software from Berkeley Open Infrastructure for Network Computing from the Space Science Lab at UC Berkeley.
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