Binding energy and binding affinity issue in docking.how to solve?
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4.6 years ago
ppnana • 0

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

docking drug design binding energy issue • 2.4k views
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4.1 years ago
db42 • 0

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 !

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