If, after molecular docking, we found that the top result (lowest binding affinity) did not interact with the key residues (but the residues were in the vicinity). Meanwhile the lower results (for example 5th or 9th Docking result) show an interaction with the key residue(s) with the same interaction type with the native ligand with acceptable distance. Should we still choose the lowest binding affinity result (to perform further validation and report) or we should consider the better binding pose?
Hi, an interesting question, I once attended a meeting where the author has first docked and then he did NMR studies, and surprisingly, the NMR pose was in 2nd cluster, not in the first cluster as he was expecting. So, he went for the 2nd cluster.
If you have already known structural information, you should use them as the standard, and compare your docking results against them. Molecular docking can be wrong/flawed and should not, in principal, use blindly.
In you case, I suggest to go for the 5th or 9th which one is closer to your structural studies rather than using lowest energy.
I agree with Ayaz Anwar , you should stick to the pose closest to the experimental data that is satisfying the main binding interactions not that with the lowest binging score.
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