Hello, I am relatively new to this field and am reading up on how to perform molecular docking between a receptor and a protein ligand. The human ortholog of the receptor is well studied (the binding domains and binding motif are identified), and structures are deposited on PDB. However, the species I am working with is only well-annotated on Uniprot. I have created a model using the SWISS-Model web server with the fasta sequence from Uniprot. From what I understand, it would be good for me to provide the active and passive residues for the docking process. The binding domain is alpha-helical, which is roughly 190 residues long. Within the binding domain, the binding motif is only 3 residues. Could I use the binding motif as the active residues, and the binding domain as the passive residues?
Thanks for you interest in using HADDOCK for your research.
Indeed, your intuition is good:
You can define the 3 binding motif residues as active.
You can also define the neighboring exposed residues as passive.
But do not forget to also define at least passive residues on the other partner (if you do not know where it binds), or active residues if you know about specific residues involved in the interaction.
Thank you for the help! Continuing with the partner protein, I suppose I can restrict the passive residues to a region if I roughly know where the interaction should occur to make the prediction more accurate.
If you are sure about your 3 binding motif residues on the receptor, define them as active
While for the partner protein, if you know roughly were the interaction should occur, then define this region as passive