Protein-protein binding affinity error

Hi All,

I am trying to determine the binding energy of ZDOCK docked protein complex comprising of two chains of a protein dimer with one chain containing a small molecule. My problem is that, when I calculate binding affinity using PRODIGY, this small molecule is not being recognized and hence the structure is rejected. Also there is a fragmentation error in the protein because it contains breaks. Kindly suggest me how should I submit my complex successfully.


Is the small molecule involved in the interaction? if not you can probably disregard it. If so, the short answer is that you can’t use Prodigy as it wasn’t trained for this even if you could in theory calculate the contributions separately using Prodigy-lig for the interaction of each monomer with the small ligand and using Prodigy for the protein-protein-interaction.