Hi! I am very new to Rosetta, and I was trying to find out a way to model the conformation of a 7aa-9aa long peptide inserted into a protein with a known crystal structure. By reading some documentation I thought loop modeling / remodeling would be the way to go. But there are quite a few methods available for loop modeling (CCD, KIC, NGK, generalized KIC etc.) and none of them specifically mentioned that it is suitable for the kind of case that I'm dealing with (a peptide insertion to a protein with known structure). Which method should I choose? How can I judge whether one method is better than the other?
By the way, do you think modeling of this kind of insertion can be precise (rmsd < 1.5A)? I found a web page showing the results of some loop modeling benchmark runs (https://guybrush.ucsf.edu/benchmarks/benchmarks/loop_modeling), but I'm not sure if my case is comparable to those.