Is it correct to compare the Haddock scores of docking analyses from different complexes (same protein with different peptide ligands with equal number of residues and a few mutations of a common motif) to determine which “complex is better” and which “complex is worse”?
This is indeed ok, but this is not a ddG (change in binding affinity)
Also it all depends on how you setup you docking (e.g. do you have good information to guide the docking).
An alternative would be, giving a good model or structure of one protein-peptide complex, only use the refinement interface and compare the various mutants.
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In addition to that you may run MM/PBSA approach - see dMMPBSA
Thank you very mucj for answering.
This answer leads to another question sorry…
The refinement interface should be used after having generated a model of the complex (e.g. by docking run) in order to optimize a structure already available ? or the the best complex structure generated by refinement interface can be used directly for the comaparison ?
Thank you again
If you have a model or structure of the wild type complex, you could simply make mutations in it and then use the refinement interface. I.e. no docking