Thursday, June 4

Protein folding and docking on the Playstation

Folding@home, as most people in the field would know, is the massively distributed protein folding simulation. As far as I remember, users around the globe can download a screen saver and contribute their idle computer processors to aid explicit (and recently implicit) solvent simulations of proteins folding and/or misfolding. Understanding this process is therapeutically important, as I have pointed out in an earlier post.Recently, a friend of mine mentioned that people had begun using Playstation consoles as a more than adequate substitute for expensive, and cumbersome nodes which are commonly used in computer clusters. The reason for this is that modern games require such heavy graphics and processor power, that the Playstations are computationally very efficient. Moreover, due to their popularity, the cost of a single Playstation is quite cheap, and the technology is very well developed. It makes sense that scientists involved in biological simulations have caught on. Folding@home and Sony have recently got together, making even idle Playstations useful.

It's not just protein folding, but the powerful playstations can be used for other computationally demanding assignments such as ligand docking. I just read that Simbiosys has released a version of their docking software for the PS3.

To lower the cost and power consumption typically associated with compound-library-screening programs, SimBioSys has also released eHiTS Lightning. This package combines the 2009 eHiTS software with IBM's Cell/B.E. chip multiprocessor, found in the Sony PlayStation 3, to achieve a 10-fold increase in computational speed. The PlayStation 3 hardware (shown) replaces some of the expensive computer infrastructure required for virtual screening programs, opening up computer-aided drug design to smaller companies previously unable to afford it.
Pretty damn cool!