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ShareScienceDaily (Sep. 18, 2006) — Applying techniques derived from classical and quantum physics calculations may radically reduce the time it takes to simulate the way that proteins fold.
It's vital to understand the shapes that proteins take on as they fold up because the shapes determine how they function, both in keeping cells running and in leading to various diseases.
Rather than calculating the motions of a protein molecule step by step, as most simulations do, a team of Italian and French physicists studied the evolution of a molecule using variational principles. The technique allowed the physicists to evaluate all the possible paths that the molecule's parts would follow and then pick out the most likely one.
As a result, they expect to streamline protein folding calculations from trillions of steps to hundreds. The improvement is significant because conventional protein folding simulations that currently require supercomputers or large PC farms could instead be solved with individual desktop PCs running variational principle calculations.
The researchers explain that the new application of the old physics method is faster because it allows them to spend less time calculating motions of molecules stuck in quasi-stable intermediate steps along the folding process. The intermediate steps account for vast amounts of wasted computation time in traditional, step-by-step simulations.
Citation: F. Pederiva et al. Physical Review Letters (forthcoming article)
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