Stanford's Folding@home project, a program that taps the idle processing time of 200,000 personal computers to elucidate the three-dimensional shape of proteins, has simulated Src Kinase, which plays an important role in many cancers. The work provides a novel opportunity for designing future drugs to combat its role in disease.
The Folding@home project predicts the intermediate states of the kinase protein by combining algorithms with the brute force of the 200,000 computers, providing more than 33 petaflops of processing power. The algorithms know the protein's start and end configurations, and determines the various ways the protein could rearrange itself to get from one end-state to the other. Certain transitions occur more frequently, increasing the likelihood they are on the actual path the protein follows in the real world.
"This is one of the first times that computation can give you something that you can almost not get from pure experiment," says University of Chicago professor Benoit Roux. "It would certainly shake things up from a drug development standpoint."
In addition, the Folding@home project has become sufficiently robust to move beyond simply identifying protein structures and toward simulating how all kinds of molecular interactions occur, says Stanford professor Vijay Pande.
From Stanford Report (CA)
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