I don't know how Foldit works internally, but I was thinking about, for example, global wiggle process.
Assumption 1: When running a global wiggle operation, the program has to calculate 'little-wiggle' for all the segments for each step of the wiggle, and it does this calculation with a sequence of segments, chosen sequentially, following a criterion, stadistic, etc.
Assumption 2: The time for a wiggle step = N*(time one little-wiggle), where N=segment_count()
Assumption 3: Perhaps there is a better solution for each wiggle step, but it should be necessary to calculate all of the combinations to know which is the best sequence of little-wiggles.
Assumption 4: I presume the algorithm to calculate little-wiggle of one segment is simple.
Approximation 1: Each little-wiggle influences subsequents, so in an only one step for N segments there is N!=N*(N-1)*...*1 possible combinations. But perhaps it is possible calculate the best little-wiggle. It would be N calculations, not N!
Approximation 2: with a limited combinations (=N) it is not a question of CPU power, but parallelization capability for little-wiggles.
Possible solution: A low power (cheap) FPGA can replicate the algorithm N times and so we have the best little-wiggle and then the (almost) best combination for each step of the global wiggle. In a FPGA it spends the same time for calculating one segment or N.
Condition: The little-wiggle algorithm should be simple to include it in a cheap FPGA.
Foldit does a wiggle, 1000 steps until it reaches an equilibrium point.
The criteria is, for example, sequential, so:
step 1 = little-wiggle(seg1) + little-wiggle(seg2) + ... + little-wiggle(segN)
step 2 = idem step1 but with state changed by step1
With a FPGA:
step1 = little-wiggle(FPGA_lw())
where FPGA_lw() = best result of parallel execution of N little-wiggles.
step2 = we send the new changed state to the FPGA and it calculates N little-wiggles again.
It doesn't speed up the process, but find a better wiggle, so equilibrium point is reached sooner, and probably with higher score.
A pci board with a little fpga would be cheap...
Does it make sense to you?