I'm working on protein-ligand docking experiment. I have an odd problem concerning how to calculate the "native pose" total_score , interface_delta and ligand_auto_rms_no_super value from rosettaligand docking experiment.
I have getted silent file after finishing rosettaligand docking experiment, and I had analysised output silent file with that contains the endpoint of every trajectory. I had also plotted interface_delta for these top-scoring structures against ligand_auto_rms_no_super and I had get a nice docking funnel. But I don't know how to calculate the "native pose" total_score , interface_delta and ligand_auto_rms_no_super value for comparing the predicting complexes. The only predicting structures docking funnel is thin for my paper. In 2008, Ian W. Davis and David Baker. "ROSETTALIGAND docking with full ligand and receptor flexibility" Fig.2.(C) had calculated "min. native", but I don't kown how to get it.
Maybe you know how to calculate it. so I hear you suggestions.
Thank you in advance.
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RosettaLigand: How to score native pose in protein-ligand docking experiment?