I have been using autodock vina and Schrodinger for molecular docking. Many times, molecules with a higher IC50 show better interactions and a lower score than the molecules with lower IC50. So, how much can we co-relate the results of docking to inhibitory effect of the ligand.
It is often said that the scoring functions for molecular docking are not particularly accurate predictors of inhibitor potency. After virtual screening of many compounds, people usually just take some number of compounds with the highest scores for IC50 testing.
We cannot get 100% correlation in between inhibitory activity and docking score. We obtain inhibitory activity by experiments and docking score by algorithms. So one can not expect 1 to 1 correlation.
If you need more information, open the attached link, you will get to know more about this particular topic, as there have been scores of discussion on RG regarding this particular topic.
Thank you
https://www.researchgate.net/post/Is_there_any_relationship_between_docking_score_and_biological_activity/1
Please go through this thread also:
https://www.researchgate.net/post/What_would_be_the_reasons_of_the_unmatching_between_docking_scores_and_IC50_values_with_references_please
Though Docking results are correlatable to activity data, SAR can be explained and a hypothesized model of binding can be generated. It's not the actives that need to be explained through docking, if rather you are able to find the reasons for inactivity of molecules for the same series through docking, it can fetch answers with better reliability
Docking basically predicts the binding energy with which your ligand can bind with the protein. Moreover, docking gives us a model of protein-ligand complex whose structure is not determined experimentally.
Correlation is just a mean to validate the docking protocol you are applying in your study. After all, it's the algorithm we are dealing with, in the docking procedure.
Dear, Rajiv,
I am agree with Adam B Shapiro. You can't rely hundred percent on predicted value (dockign score). Sometimes, it varries and depends of types of scoring function used during algorithm develoment. But, I think you can cross check with different scoring functions. You, may get some idea about your problems.
use docking when you have 100s of compounds. docking is just a checking whether the protein and ligands are having any interactions. if you have only one or two compounds and wanting to do docking it may be waste of time. go directly to assays.
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