I would like to ask if I can report the values of binding energies obtained using autodock Vina as mean +/- standard deviation? I docked the ligands in the receptor 5 times (5 trials). Thank you!
Yes if you have the docking done 5 times you can use the binding energies reported in Autodock Vina along with the standard deviation. They should correlate with experimental binding affinities with of course some room for error.
hello dr. Debarati Dasgupta thanks for your response. I am only doing in silico screening as part of my protocol. I've searched through journals but the binding affinity values were not reported as mean +/- standard deviation so I was wondering if I can report the binding affinity from autodock vina as mean+/- SD.
It is always a good measure to do the docking and rescoring using separate scoring functions, that can help in adding confidence to the quality of docked poses you generate.