SkeleDock
HTMD1.13.8/Rdkit2018.03.4
Assumed pH 7.4
An initial conformation was generated from the smiles using RDkit.
Only used the best starting point that SkeleDock suggested
We used SkeleDock, an in-house algorithm which finds common dihedrals between a template molecule and a given ligand and mirrors them
so that the ligand torsion angles match the values in the template. For each molecule in the test set, we tried all 20 provided molecules in the stage 2.
The pose which had a greater percentage of the ligand volume overlapping with a template was selected as the best pose.
Yes
Yes
SkeleDock KDeep
HTMD1.13.8/Rdkit2018.03.4/KDeep
Assumed pH 7.4
We used SkeleDock, an in-house algorithm which finds common dihedrals between a template molecule and a given ligand and mirrors them
so that the ligand torsion angles match the values in the template. For each molecule in the test set, we tried all 20 provided molecules in the stage 2
and we picked the best according to shared excluded volume. Then we used KDeep (at playmolecule.com) to evaluate the free energy.
Yes
Yes