1479-1-bbrsx-PosePredictionProtocol.txt

Name

SkeleDock

Software

HTMD1.13.8/Rdkit2018.03.4

System Preparation Parameters

Assumed pH 7.4

System Preparation Method

An initial conformation was generated from the smiles using RDkit.

Pose Prediction Parameters

Only used the best starting point that SkeleDock suggested

Pose Prediction Method

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.

Answer 1

Yes

Answer 2

Yes

1479-2-ehiuo-LigandScoringProtocol.txt

Name

SkeleDock KDeep

Software

HTMD1.13.8/Rdkit2018.03.4/KDeep

Parameters

Assumed pH 7.4

Method

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.

Answer 1

Yes

Answer 2

Yes