I was provided with a DNA–protein docked complex for molecular dynamics (MD) simulation, which I have now completed. I would like to identify the key binding residues or domains involved in the interaction. What analyses should I perform to determine the binding interface?
Is hydrogen bond analysis and binding energy calculation (e.g., MM/PBSA or MM/GBSA) appropriate for this purpose? Or is MD not typically used to pinpoint binding residues? What other methods or tools can I use to accurately identify the binding residues between the DNA and protein?