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 best starting point that SkeleDock created

Pose Prediction Method

The provided fasta sequence was used to look for homologs in PDB. After aligning the closest homologs, we selected those
whose cocristallized ligands had a common scafold with the test molecules and that matched the mutations pointed out in the challenge description.
Those were 3IEJ and 5QBY. All ligands were tested using SkeleDock against both templates and the poses which had a greater shared occupancy with the template was selected.
SkeleDock is an in-house algorithm which finds common dihedrals between a template molecule and a given ligand and mirrors it
so that the ligand matches the values in the template.

Answer 1

Yes

Answer 2

Yes

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 it
so that the ligand matches the values in the template. The best pose was selected and used as input for KDeep (at playmolecule.com) to evaluate its free energy.

Answer 1

Yes

Answer 2

Yes