I am docking 1 protein with 5-6 ssDNA sequences. How do I find out which is the best ligand? as you don’t give binding energy for DNA-protein docking.
Thank you
We don’t have a solution for this I am afraid…
If the protein is the same (i.e. a constant), scores might be better indicative of preferences for binding.
But this has never been tested for protein-ssDNA.
The only advice would be to find systems for which you know the answer and test if you can fish out the correct sequence.
Not easy in our hands…