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

Matt K. 5xx7xx at gmail.com
Sat Aug 8 10:37:18 PDT 2020


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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