I am working on Protein-DNA/RNA docking and using HADDOCK 2.4 server, but I couldn't understand the relation between HADDOCK score and binding enthalpy (if there is any). I want to find the strength of the interaction between a protein and the DNA/RNA molecule. Can someone help me out?
Hi Nabajit,
There is no relationship between HADDOCK score and binding affinity. You should treat the HADDOCK score as a guide for the best result within a given docking simulations. Because the score is based on the type and number of restraints you use in the docking simulation, the score will vary between simulations. This means you should not think of the score as a metric for how well two molecules interact and you should not compare scores between simulations.
There is a very good message board associated with HADDOCK and related software (https://ask.bioexcel.eu/c/haddock/6), and this point has been addressed there (https://ask.bioexcel.eu/t/problem-with-interpretation-haddock-scores/5038).
Best,
Mike
Michael Latham thank you for the detailed answer.
Is there any other way I can find the binding enthalpy of the docked complex (Protein-Nucleic acid)?
Experimentally, isothermal calorimetry (ITC) is the best way to do that. I think there are ways computationally, but those are outside my area of expertise.
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