Hello, i want to ask a question about peptide-protein docking.
There is no PDB structure for my peptide because i edited one of the amino acids in the sequences, is it ok if i used uscf chimera to draw the structure? and after i draw the structure of my peptide is there any further step to prepare the peptide before we input it on the haddock server for docking?

Thank you.

You can also use Pymol to build the peptide in various conformations and give an ensemble of structures as starting point for HADDOCK as described in our protein-peptide docking paper.

Some instructions are available at:

And relevant papers:

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