Question: Binding energy and binding affinity issue in to solve?
gravatar for ppnana
24 months ago by
ppnana0 wrote:

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

ADD COMMENTlink modified 18 months ago by zappy0 • written 24 months ago by ppnana0
gravatar for zappy
18 months ago by
zappy0 wrote:

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 !

ADD COMMENTlink written 18 months ago by zappy0
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