A reviewer asked me to answer his question which I didn't understand exactly what he was looking for, knowing that I had calculated all the necessary docking parameters (binding h, binding energy, score, inhibition constant and interaction distances.
The question is: "In order to understand the contribution of the various interaction mechanisms, their values should be presented and discussed (how is the score function composed?)". Is there anyone who can help me understand his question?
Simulate (MD Simulation) the Docked complex and then calculate the binding free energy using MM/GBSA or MM/PBSA it will give you contributing every energy parameters in binding free energy.
From the reviewer's question, it seems they are interested in gaining a deeper understanding of the different interaction mechanisms involved in the docking process and how they contribute to the overall score function. The score function is a key component in docking software that evaluates and ranks different ligand-protein interactions based on their predicted binding affinity.
Thank you for your detailed answer to my question M. Jamoliddin Razzokov.
I'd like to answer my second question, which was asked by another reappraiser as part of the same work.
The question is: Make a table and include the protein - ligand interaction values in molecular docking analysis discussion part?
Is he talking about distance values?
Thank you again.
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