The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to http://www.bonvinlab.org/software/haddock2.2
Hi, i have some questions.
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
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?