Is running Folding@home / Rosetta@home beneficial?

Rather than get into the details, I'll make the meta-level point that the impact of your action here is likely to be very small in one direction or another.

At best, you are one more computer in a network of millions*; at worst, you've added a tiny amount of pollution to the air, which might take a few minutes to an hour off of humanity's collective lifespan, if we stick to Gwern's reasoning -- you might waste more human life in the course of spending time to install the software than you would actually running the program.

Meanwhile, the "indirect costs" are based mostly on money you could otherwise donate to charity, a consideration which could come up every time you spend money on anything (and which is generally better to ignore unless you're making a big spending decision; I wouldn't worry about $10/year).

Given the complexity of the issue (e.g. trying to calculate your computer's extra electricity usage, evaluating the expected value of papers produced through FAH), I would recommend against trying to make a serious calculation of your impact. As with many questions people ask in EA spaces, "don't worry about it" is a reasonable answer.

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*There are only about 100,000 machines in the FAH network right now, but many of those were designed specifically for high-performance computation; I'd be unsurprised if an average home machine contributed one-millionth or less of the project's processing power.

Since this post has gotten very little traction, I wanted to let you (orenmn) know that at least I found it valuable and interesting!

One element of this I'd like to understand better is the trade-off between donating your own compute (i.e. donating money you're spending on electricity) compared to donating money directly to a protein folding effort that utilizes cloud computing. In general, how do the hardware savings of using an existing device compare to the greater efficiency of cloud computing? Is the key innovation of Folding@Home that they're able to obtain in-kind electricity donations from people who wouldn't otherwise donate money to fund the effort?