After running Flexpepdock, I want to calculate the binding affinity of peptide (ligand) on protein (its acceptor).
Can someone suggest me the method?
Thank in advance and best regards,
The FlexPepDock has a rescoring mode (See https://www.rosettacommons.org/docs/latest/flex-pep-dock.html). Using the -flexpep_score_only flag should give you a number of statistics about the binding, including an estimated binding affinity, without doing any redocking of the compounds.
Another way to go is to use the interface analyzer (https://www.rosettacommons.org/docs/latest/interface-analyzer.html) which is a general application for looking at the interactions of two molecules, but that's less peptide-binding specific.
Thank you so much for your help and your explanation. I got it clearer.