I ran docking to check the interaction between three molecules (two proteins: receptor and its ‘ligand,’ and a peptide) to check whether the peptide disrupts the receptor-‘ligand’ interaction or not using multibody docking and got really some interesting results. However, I wanted to know whether these results can be used to interpret competitive binding or not. I read some papers where the competitive binding has been defined using docking as a protocol, but it is generally used for a protein-ligand system. If yes, then how can I compare the binding affinities/ HADDOCK score?
There is no correlation between docking score and binding affinity I am afraid…