Macromolecular Modeling Blog ™

Rosetta@home is a screen saver application that utilizes the BOINC distributed computing infrastructure and allows the running of the Rosetta software to conduct protein folding, docking and design simulations using the massive power of over 600,000 cpus world wide. ( see YouTube video )

The combination of such massive computation power with the cutting edge abilities of Rosetta in modeling has led to numerous results and to the publishing of papers as: “Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.” 

Users of Rosetta@home are also acknowledged specifically in papers resulting from the usage of  this system.

We thank all the Rosetta@Home users worldwide who have generously donated their computers to support our research, particularly users ‘‘StevenK’’, ‘‘Administrator’’, ‘‘QuickBeam’’, ‘‘devzero’’, ‘‘raptur’’, ‘‘cyclisttgb’’, ‘‘borekv’’, ‘‘yopjpeg’’, ‘‘orion2598’’ and ‘‘MK_I’’ who produced low-energy models for our submissions.

Folding@home is another such venture which uses the GROMACS package mostly to engine the folding. It has received much attention for harnessing Sony’s PS3 machines to participate in the protein folding efforts. 

This Breakthrough into home entertainment systems put Microsoft between the rock and the hardcase. A year ago, Different reports indicated that Microsoft was going to adopt Rosetta@home to run on its Xbox-360 machines, including Dr. David Baker himself the founder and head scientist of the Rosetta@home project and a leading figure in protein science, which commented on this issue in his Rosetta@home journal. Others indicated Microsoft might opt for Folding@home.  

I just met yesterday with Tony Hey, the corporate vice president for technical computing at Microsoft, to discuss this possibility further. Tony and Microsoft have been incredibly supportive of our efforts so far, and he is going to help us try to make this become a reality in the not too distant future.

In the meanwhile more than a year have passed and about 12 million Xbox360 cpus are waiting idle. Isn’t that a shame ?!

On a different note, but on the same page Adam Kraut tells us that the Pittsburgh Supercomputer Center presented a demo last year of running an interactive MD simulation on a Cray supercomputer using a Wiimote as an interface to guide the simulations. 

Are home gaming consoles the future for computational structural biology ? how do you fold proteins with your cpu’s spare time ? Tell us in the comments. By Nir London