I had some molecules, which I had found active by performing Molecular Docking studies based on the docking scores and further performed MD simulation studies to predict the stability of the Protein-Ligand complexes. How far is it important and the necessity to perform MM/PBSA and MM/GBSA calculations after molecular dynamics? Should it be performed before or after the dynamics studies? I will be grateful if anyone can help me regarding this question.
Thanking you in advance.
Dear Das,
The MMGBSA can be performed before and after MD simulation, and by this method, you will have comparative results for free energy.
It is not mandatory to perform, but of course, it gives an extra edge to prove your results for excellent effectiveness at the docked pocket.
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