Dear researchers,
I am currently working on molecular docking of urease enzyme with few numbers of inhibitors by using autodock.
My questions are:
1. How do we confirm all the steps performed in the docking are correct and the values obtained are valid?
2. In the docking process, I performed 100 runs and the grid box was not only focusing at the active site of urease. Thus, the size was bigger. How do we compare which conformation is the best?
Shoud I choose the conformation that closer to active site even though the binding energy was lower?
Thank you.
Hi Nurliana Farhana Salehuddin ,
You can select the lowest binding energy confirmation with 0 RMSD. which is usually come out of total confermations.
hi
you can chose the the conformation which if it superimposed with reference ligand with RMSD lower than 3.
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