Question: Binding energy and binding affinity issue in to solve?
gravatar for ppnana
2.6 years 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 2.1 years ago by db420 • written 2.6 years ago by ppnana0
gravatar for db42
2.1 years ago by
db420 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 2.1 years ago by db420
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