stage2_vina_score
smina
--exhaustiveness 50 --seed 0
This uses the AutoDock Vina scoring function built into smina.
Unlike the stage1 results, with this set we include poses of ligands
docked to their corresponding stage2 crystal structure.
We did not cross-dock other ligands to the provided stage2 structures.
The poses selected for scoring were those with the best (lowest energy)
score - we did not use the RMSD to the know structure.
stage2_vina_score
smina
This field intentionally left blank, but not really since the validator won't accept a blank field.
Waters were stripped from receptors. Protonation was performed with openbabel.
--exhaustiveness 50 --seed 0
smina was used to dock to a selection of reference
receptors (same poses as stage1) and to re-dock the provided stage2 complexes.
A minimized pose generate from the crystal pose was generated as well.