Okie, if let’s say I have the native structure of a protein-peptide complex, but I wish to only change 1 or 2 residues of the peptide, do you think it might still give me a relatively accurate result.? since I presume that there shouldn’t be major changes to the secondary structure of the peptide.
This is a perfect scenario to use FlexPepDock, create the model of the mutant peptides (e.g. using fixed backbone design) and then run flexpepdock to refine the structure and see if the mutations can be accommodated.
Good luck.
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