Are you doing self-docking or are you analysing the models as-is? Not all binding poses in the PDB are realistic and things like atomic clashes have a massive energy penalty.
Have you looked at the model in the electron density? You can also try the pdb-redo version op the same pdb entry to see if that gives a more sensitive binding energy.
HTH,
Robbie
On 28 Jun 2023 17:39, Thripthi Shenoy <thripthishe...@gmail.com> wrote:
I am performing docking studies for some of the protein structures from PDB using AutoDock Vina. Some of the ligands are giving binding energy as positive integers (eg. 435 kcal/mol). I tried rectifying the issue best to my knowledge. I would be grateful if someone could explain to me the reason for such a result.Thanking in advance,Thripthi S.
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