Ok, Ralph/Rosetta may not support gpu in the next future, but is not possible to have a multi-threads wu?? With 8 cores cpu, may have great improvement...

Multi-threading would be a headache to support for no practical gain. Protocols typically function by taking a single structure through a series of steps, which means there's choke points which would limit the speed increase you'd get from multithreading. Rosetta is really set up for trivial parallelism. Instead of multithreading a single structure, the better way to handle multiple CPUs is to run multiple structures at the same time, and the easiest way of doing that is to run multiple independent instances of the program. (Which happens to be a good match for the boinc setup.)

If you want to make full use of your 8-core CPU, go into your boinc computing preferences, and increase the "On multiprocessors, use at most" settings. This way you should crunch on eight work units at once (one for each CPU). Although each will run at about the same speed as a single work unit on a single CPU, you'll still come out ahead credit/scientific-result-wise of if we implemented multi-threading.

Thanks for the answer!! :-)