Hello,
I want to dock a cyclic peptide on a target, with the cyclic peptide chain being defined as UNL in the PDB. When using the online Haddock tool, I define the cyclic peptide PDB as Ligand, and turn on the cyclic peptide button (as shown in the picture below). Question: Is the cyclic peptide protocol running, even though I defined the peptide PDB as Ligand and not as Peptide?
Many thanks
). Question: Is the cyclic peptide protocol running, even though I defined the peptide PDB as Ligand and not as Peptide?
No it won’t. This only works with amino acids, i.e. standard supported ones defined as ATOM
Dear Prof. Bonvin,
Can’t we make docking for cyclic peptides with non natural amino acids?
Best,
Ahmed
The only one we are supporting are the ones listed on the following page:
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