Hex shows binding energy of -219.89, while autodock showed for the same -9.89.
Can someone clearly state how to defend this difference in the binding energy?? Is it the algorithms they follow that cause this difference??
Kindly elaborate.
This difference is usually due to the differences in the forcefields and parameters used by the two programs. They may have also mapped different residues in the cavity during ligand rotation and translation. If you want to compare the two results then list the active site residues with which your ligand makes an interaction. Similarities or differences can explain the difference in the binding energies. And also check the units.
the difference in binding energies may be due to various reasons. it would be good if you focus on ranking of the ligands and classify as strong binder and weak binder, when comparing the results of two different packages.
difference in scoring parameters also might be the reason.
I want to ask another question in this regard. What are the default units of the binding energies that we get in both Hex and Autodock.
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