We did a virtual screening of database using autodock vina. We started ranking the molecules based on docking score and observed three molecules of different chemical structure with same docking score (-11.2, -11.2, -11.2 kcal/mol).
Is there any possible way to increase the significant figures of docking score for ranking the molecules??
Also, how the compounds with different chemical structures can give same docking score??
Thanks in advance.
It is not possible to increase the significant figures of the docking score output by AutoDock Vina, as the program provides output with a fixed number of decimal places. However, you could try running multiple docking runs and averaging the results to get a more accurate score.
Regarding the compounds with different chemical structures giving the same docking score, this could occur due to various reasons. One possibility is that the docking program is not sensitive enough to distinguish subtle differences in the binding interactions of these compounds with the protein receptor. Another possibility is that the protein receptor has multiple binding sites, and these compounds are binding to different sites with similar affinities. It's also possible that the scoring function used by AutoDock Vina is not robust enough to differentiate between the binding energies of these compounds. It is important to further analyze and validate the results obtained from virtual screening experiments to ensure the reliability of the hit compounds identified.
Susanta Roy Thank you for addressing the query. We have tried the same. Surprisingly, all the three docking runs gave same docking score with autodock vina.
Try to confirm with AutodockTools software which has more accurate scoring function compared to vina...
regards
Jobin Thomas Do you have any codes for docking multiple ligands in autodock. Thanks in advance.
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