I want to dock Nortriptyline into hDAT model as the authors ofArticle A high quality homology model for the human dopamine transpo...
did.I prepared the structures of ligand and protein as the article said. However nortriptyline posed in different way in my case.
Could it be because I'm using a different program for ligand optimization (Avogadro instead of MAESTRO)?
Could the new version of Vina give another result?
Or I did mistakes when pdbqt-files were being prepared?
Because you don't know what configuration was used for ligand optimization, you can't exactly replicate the same pose as in the literature.
Optimization with different tools will result in different docking poses, and different versions of the same tool will also influence the binding pose as new features that contribute to binding pose prediction are added.
If it docks smoothly, it usually means you didn't make any mistakes when preparing the files.
Yasir already got straight to the point. And I agree that the different ligand optimization approaches will yield different outputs. It might be wise not to look at the top 1 pose only but to consider further poses for comparison as well.
Also just want to add that Vina's docking algorithm is non-deterministic which means that in some cases it will fail to find the minimum of the scoring function. If it's just bad luck and the minimum actually does correspond to the correct (expected) docking conformation then you could try with a different seed, a smaller search space, or use a higher exhaustiveness setting.
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