Understanding how proteins self-assemble ("protein folding") is a holy grail of modern molecular biophysics. What makes it such a great challenge is its complexity, which renders simulations of folding extremely computationally demanding and difficult to understand. (See Scientific Background for more details about what are proteins, why do they fold, why this is so difficult, and why do we care). Our group has developed a new way to simulate protein folding ("distributed dynamics") which should remove the previous barriers to simulating protein folding. However, this method is extremely computationally demanding and we need your help (see below). We have already demonstrated that our distributed dynamics technique can fold small protein fragments and protein-like synthetic polymers. The next step is to apply these methods to larger, considerably more important and complicated proteins. Unfortunately, larger proteins fold slower and thus we need more computers to simulate their folding. While the alpha helix folds in 100 nanoseconds, proteins just a little larger fold 100x slower (10 microseconds). Thus, while 10-100 processors were enough to simulate the helix, we will need many more to simulate these larger, more interesting proteins. HOW YOU CAN HELP To achieve a significant speedup, we need lots of processors in a given run. Also, since a single run does not tell us much, we need to simulate several runs (10 runs would be a good start) per protein. Thus, we need lots of processors. By running our client that uses the Mithral CS-SDK, you can lend us your machine for as long as you like. The client allows you to run for as little or as long as you like. Even a single day's worth of running is helpful to us. Folding@Home 2.0
