pro tools is software. compatibility will have nothing to do with the hardware beyond it having to be x86 (which all are). You just need a windows OS.
If you are starting from scratch, read this, then post a reply with all the information we need to help you. First and formost is your budget. Seriously, I could recommend a CPU and mobo that is "compatible with ProTools" for $70 or I could suggest a more powerful CPU and motherboard for $1,500.
Anyway, here's the link: http://www.tomshardware.com/forum/261222-31-build-advic...
Hmm...I was under the impression that ProTools (which I certainly KNOW is software). I was under the impression that certain chipsets freaked out with PT so I was throwing that out there in case someone on the boards built a home brew system specifically for use as a PT DAW. If that was the case, I would have no problem building the exact same system. Thanks