Dear HADDOCK community,
I would like to dock a 15-residue peptide to a receptor, using the HADDOCK2.4 webserver. I have few questions:
- Is the peptide allowed flexibility? If yes, are only the sidechains treated as flexible or also the backbone? We suspect that this peptide undergoes some order-to-disorder transition during binding.
- Does the webserver submission form allow to tune the flexibility of the peptide. If so, could you suggest me which options should I consider?
- The receptor has an acylated residue. This residue is part of the binding pocket and it might play a role. Will the acylated residue be simulated or just disregarded, being a non-standard amino acid?
Thank you for your help,