A dock validation protocol was conducted with the native ligand and an RMSD value less than 2 Angstrom was obtained.
The same validation conditions was applied during that of the database (which contains various compounds) docking but the compounds present in the database mostly dock outside the established wall.
What could be the problem or reason behind this?
Should I he worried?
Please see the attached image !
Either the ligand is too large and doesn't "fit" into the box constraints or there are atomic clashes with the binding site residues
Thanks for your contribution @Fidele Nite-Kang. In the case of the ligand being too large and doesn't "fit" into the box constraints, do I have to be worried about the results sir?
You've got to "train" your docking procedure or validate the docking protocol so as to identify the ideal parameters for the box. This could, for example, be done by removing the native ligand from the box, docking the native ligand back into the site and comparing the X-ray ligand with the docked ligand. In the case, for example, where the top scoring pose give a low RMSD for the X-ray versus docked ligand, you can retain those box parameters and use as standard for docking a ligand library.
In the question description sir, I stated that a dock validation protocol was conducted with the native ligand and an RMSD value less than 2 Angstrom was obtained.
The same validation conditions (the ideal parameters) was applied during that of the database (which contains various compounds) docking but the compounds present in the database mostly dock outside the established wall.
Sir, I guess I will go with your previous answer - "the ligand being too large and doesn't "fit" into the box constraints". But should I be worried if the above is true?
@Fidele Ntie-Kang
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