Binding energy and binding affinity issue in docking.how to solve?

Question

[ppnana]

I have been doing docking for a compound with a protein using autodock but I am getting the results as following the pose with the best binding energy have lower Ki value and as the binding energy is getting poorer then the Ki value is higher. example

-8.18       1.01 uM (micromolar)
-7.92       1.57 uM (micromolar)
-6.61       14.39 uM (micromolar)
-6.31        23.87 uM (micromolar)

please suggest what could be the potential problem and what could be the solution. ASAP

Answer 1

[db42]

I think your data is coherent. The lower the binding energy the better the ligand (I think). So clearly your -8.18 has the lowest Ki 1.01 uM. Concordant !