So, is there any way of knowing about the on-site build protein beforehand, or will we just be asked about the general concepts behind all proteins and how they apply to that specific protein?
Generally, the proteins used for onsite are listed online in resources on MSOE's website, but they won't tell you the exact sequence range they want you to model on the website - that's what you find out when you get there. I don't think I've competed in seasons where I've attended enough of a sample size of invitationals within that season (unfortunate conflicts) to know if the invitational onsite that MSOE distributes is the same for them all or no. Honestly, it's kinda unpredictable, which is the beauty of the onsite model since you have to be really familiar with Jmol as well as attentive to details in terms of trying to create a great onsite.
EDIT: I checked the website and currently as of this post it looks like only a single CRISPR-Cas9 protein is listed for the different levels of onsite (the same pdb file for them all too). Generally, there should be four different proteins, I'm not sure if it's something they were going to do yet haven't changed on the website (which may be unlikely since it looks like the whole site seems to have been built up, possibly minus some things that I haven't poked around for yet) or if they just want to do a different sequence for each level of onsite... *shrugs*