I am using MOE 2010 to dock a protein with a ligand, how can I calculate the binding energy of the ligand to the protein of interest from the docking results?
Thank you
There is so many ways to do so. first, it will essentially give it in E_Score tab in the database file (.mdb extension file). Second, If you are very peculiar about the energy then using Database Browser to browse to that particular docking pose and hit the button of Potential energy under the compute tab on your window.
Thank you so much Arvind. The second option will give me the total energy of the protein bound ligand. Should I subtract this from the summation of the individual molecules (protein+ligand) to obtain the binding energy?
On the other hand, does the E-score value refers directly to the binding energy of the corresponding pose?
Thank you.
Honestly speaking its E-Score is combination of parameters but potential energy is more directed to its free energy or you could somehow say binding energy.
Hi,
Take a look to this tutorial.
https://scs.illinois.edu/system/files/inline-files/SCS-UIUC-moe-tutorial-dock-05-2011.pdf
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