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Home > iSGTW 30 April 2008 > iSGTW Image of the week - Shave hundreds of years off your research life


Image of the week - Shave hundreds of years off your research life


The villin protein is presented here in two superimposed forms: the first predicted using BEMusE on EU-IndiaGrid, and the second measured experimentally. The similarity demonstrates the algorithms accuracy.
Image courtesy of Stefano Cozzini, EU-IndiaGrid

BEMusE— or the Bias-Exchange Metadynamics Submission Environment—is a grid-enabled tool able to fold a 36-residue protein in less than a year of single CPU time: a vast improvement on the hundreds or thousands of CPU years required by other grid-based techniques.

Bedazzling researchers with its accuracy and speed, BEMusE scooped the poster prize at December’s eScience 2007 conference.

Biased towards grid

BEMusE evolved from the Bias-Exchange Metadynamics algorithm, developed by Alessandro Laio and Stefano Piana, which folds proteins with increased accuracy.

“It was immediately clear how much the algorithm would benefit from the grid,” says BEMusE researcher Stefano Cozzini, of Democritos in Italy.

The BEmuse team, composed by Riccardo Di Meo, Fabio Pietrucci, Alessandro Laio and Cozzini, ported the application to EU-IndiaGrid, and the results have been extremely promising.

“Our simulations, run on the grid, were able to explore protein conformations at a speed comparable to simulations run on HPC resources using MPI,” explains Cozzini.

“In the original MPI implementation, all CPUs start at the same time, have the same hardware and similar input files,” he says. “With our grid-enabled approach, exchanges are still synchronous, but the CPUs arrive at different times, have different speeds and may be mixed with others that ran for very different intervals.”

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