I have a scenario where I have a peptide-protein complex. I would like to thread a series of sequences over the peptide, then minimize the peptide-protein complex. The idea being, I would like to tell which threaded-peptide-sequences would be the "best" binder predictors. Or at least be able to segregate between potential non-binding sequences and binding sequences.
I've been looking at the backrub protocol. Would this be an appropriate application? I don't see immediately how I can thread the sequences over the peptide with this application then.
Then I've looked at the threading protocol. This looks like I can thread the series of sequences over the peptide, but I'd need fragment files for each new sequence? I don't exactly want this because I know the starting conformation of the peptide (even if I'm attempting to vary the sequence).
Then I've seen the fold and dock protocol. This looks decent because I know the starting conformation of the peptide when docked to the protein, but again, how can I thread a series of sequences over the peptide? And it a full fold-and-dock overkill?
Any advice would be greatly appreciated.