ADL: Getting very similar docking results for multiple unrelated proteins (Vina)

Diogo Martins diogo.stmart at gmail.com
Sat Aug 8 11:45:13 PDT 2020


Hello,

It's good to be suspicious of docking scores. Larger molecules almost
always have better scores, maybe some form of normalization by size, such
as dividing the score by the number of atoms, could make them a little more
informative.

Best regards,




On Sat, 8 Aug 2020 at 10:39, Matt K. <5xx7xx at gmail.com> wrote:

> Hello everyone,
> I'm doing a screen using Vina and I got really suspicious when I got very
> similar results for three different sites on my protein, so I also ran four
> unrelated proteins chosen at random from PDB, and results are also very
> similar. Most molecules are within the same percentile (or off by one or
> two percentiles) across all proteins.
>
> The molecules used for docking are from the ZINC15 database, specifically
> the "world" subset. https://zinc15.docking.org/substances/subsets/world/
> I've downloaded them in mol2 format, split into separate files using
> OpenBabel and prepared them using the MGLTools script "prepare_ligand4.py"
> (this one here:
>
> http://wind.isi.edu/marbles/assets/components/workflow_portal/users/lib/MGLTools/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py
> )
> by using the "bonds_hydrogens" repair option.
>
> Protein preparation was done manually in Autodock Tools by deleting
> ligands, deleting water, adding all hydrogens, merging non-polar hydrogens,
> adding Kollman charges, spreading charge deficit over all atoms in residue,
> and choosing as macromolecule.
>
> Grid box for each protein was chosen manually with size usually 30x30x30
> angstrom set in each protein's primary binding site. Vina exhaustiveness
> was set to 12.
>
> What am I doing wrong here? Why are my results so similar across unrelated
> proteins?
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