Protein protein docking

Then you need to provide restraints. If you don’t have any experimental data that you can convert into distance restraints and give as unambiguous or ambiguous restraints, you can provide active/passive residues that you think are important for the interaction between the protein and the peptide.

Finally, if you really have no information, you can try an ab initio docking by turning on the Center of mass restraints parameter under the “Distance restraints” section of HADDOCK Guru interface.

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