Hi,
I’m a master student and my goal is to assess whether a fictional ligand would interact well with a receptor, and if it interacts in the same way as a known ligand (I want to see if my fictional ligand would have the same properties).
I have run jobs (fictional ligand on my receptor) on the haddock web server and gotten the binding energies from the pdb files from the results. I am now running jobs with my known ligand to get the binding energies.
I will be plotting them in two histograms to look at the occurrences of different energies. From what I understood I can compare binding energies even though they don’t mean anything by themselves, if the protein is the same.
Does this mean that a histogram of binding energies for only my fictional ligand won’t give me any insight on my fictional ligand’s performance if I don’t compare it to a known ligand ? Or can I look at the distribution of energies (very negative histogram, very wide/narrow distribution…) and still get an interpretation ?
I’m very new to this so any help would be greatly appreciated.
Thanks in advance !