Hello,
I was wondering how does del G and Kd values for a protein-protein complex change after simulating the complex. How comparable is Prodigy with MM-PBSA and MM-GBSA analysis of the same simulated complex?
I don’t have the answer to this, but it would be nice if someone was to take the challenge and actually do the comparison on a large set of complexes…
It will take quite some more time than running PRODIGY 