Autodock Vina baseline
docking performed with smina static binary available at https://sourceforge.net/projects/smina/files/ with default scoring function, conformer generation performed with rdkit via https://github.com/dkoes/rdkit-scripts/rdconf.py.
rdconf.py was used with the defaults except --maxconfs 1 was specified. Water was left in the starting receptor structure for docking.
for each SMILES input, a single conformer was generated via rdkit using the UFF force field. All compounds were docked by smina using the Autodock Vina default scoring function.
Reference ligands were used to define a box, and then 8 Angstroms of padding were added to each face of that box to define the search space for docking. The random seed was set to 0 and the exhaustiveness was set to 50. The default number of final conformers was used, which is 9. To be added to the final prediction set, a pose was required to differ from poses already in the set by more than 0.5 RMSD in order to ensure pose diversity.
Compounds were docked with smina using the Autodock Vina default scoring function. Docked poses were ranked by their predicted affinities. The best-scoring pose was chosen, and subsequent poses were chosen in order of rank if they differed from existing poses in the chosen set by greater than 0.5 RMSD until at most 5 poses were chosen.
No
Yes