I am trying to do protein-peptide docking using easy interface. I have experimental data to define active residues for the peptide but not for the active residues in protein for my peptide. However, there are few evidences defining active residues for one of the protein subtype I am docking while there is none evidence for the another subtype. But from the previous evidences, a stretch of 10-15 amino acids is identified to form an interacting site for the peptide. In this case:
- should I define the whole stretch of 10-15 amino acids as active residues?
- should I define the whole stretch of 10-15 amino acids as passive residues?
- should I define the certain amino acids amino acids based on evidences from other protein subtype as active residues?
- Or, any other advice?