Not all Linux distributions are created equally - which is why there is so much variety. The focus for the Ubuntu team is the desktop, of course. In my personal experience, I find Ubuntu to be less stable and more buggy than other distributions I've used; I believe this is because its aggressive development and release cycle.
I don't know if it'll improve folding performance, but CentOS is more relevant on the server side and would be an asset to learn. There should be excellent resources to help optimize a CentOS server.
Like any OS, Linux benefits from optimization. Kill any daemons you don't need. You may also consider compiling the kernel yourself to remove unnecessary features and improve performance.
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