First, how can i get the binding energy of ligand to protein in docked structure obtained from HADDOCK?
Second, what is the definition of HADDOCK score? What is the formula? Any reference?
Third, any suggestion to superimpose two binding mode of complex and calculate the RMSD of pose?
Would appreciate if anyone can kindly explain
*UPDATE
Today, i just read skim through the journal “Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2” . In the journal, it was stated binding affinity was predicted using ligand-based binding affinity predictor. Just curious the data set used in the journal is it in SDfiles?
I would like to ask you, if it is the right decision to use refinement interfaces of HD2.2 or HD2.4 for binding energetics assessment between a protein and cofactors? (the structure is resolved and we know where the 2 cofactors are binding and how they are placed in the binding pocket) Is there a kind of recipe which settings should be adjusted for this kind of calcualtions?
We never really benchmarked HADDOCK for this purpose, but it should be a viable approach.
Some related work on protein-ligand binding affinity can be found in