I'm quite new to rosetta design i'm trying to understand all the possible options to design a DNA-protein interface.
I was using rosetta_source/test/integration/dna_interface_design/design.script but I have a couples of questions on the output:
what is a "MultiState Fitness" could please give me an idea of the range of this value?
which is the difference between "SeqScore(binding)" and "SeqScore(bound)"?
which is the difference between "Specificity(binding)" and "Specificity(bound)"?
and the binding energy calculated at the end is refered to the complex formed by the new DNA and the best sequences for the protein?
Any details/suggestions on the protocols to calculate protein-DNA interface will be very welcome!