1147-1-kycay-PosePredictionProtocol.txt

Name

Maestro 2018/Amber18/Pyemma 2.5.4/Openeye Omega 2018/Openeye Docking 2018

Software

Maestro 2018/Amber18/Pyemma 2.5.4/Openeye Omega 2018/Openeye Docking 2018

System Preparation Parameters

Assumed pH 5

System Preparation Method

Maestro's prepwizard was used to assign protonation states in 5.0 pH solvent. Crystal waters with more than 2 hydrogen bonds to non-waters were kept. The apo system was ran in the Amber environment FF14SB and solvated for TIP4P-Ew water parameters with charges added according to 5.0 pH. The system was minimized and equilibrated at NPT with a non-bonding cutoff of 10 Å.

Pose Prediction Parameters

Chemgauss4 Scoring Function
Standard Search Resolution

Pose Prediction Method

MD simulations were used to generate receptor conformations. Using Pyemma, TICA K-means clustering was done on selected features to extract representative structures for docking. Default openeye docking parameters were used to dock to an ensemble of 10 receptors. Box enclosing active site was constructed using maximum and minimum coordinates of the whole protein. The pose with the minimum score was selected.

Answer 1

No

Answer 2

No

1147-2-j8mcv-LigandScoringProtocol.txt

Name

Maestro 2018/Amber18/Pyemma 2.5.4/Openeye Omega 2018/Openeye Docking 2018

Software

Maestro 2018/Amber18/Pyemma 2.5.4/Openeye Omega 2018/Openeye Docking 2018

Parameters

Omega Maximum # of Conformers=800
Omega Canon Order=False
Omega Sample Hydrogens=True
Omega Energy Window= 15.0 kcal/mol
Omega RMS Threshold= 1.0
Omega Range Increment=8

Method

Ligand conformers were generated using Openeye’s OMEGA toolkit. Other than parameters specified above, default OMEGA parameters were used. Ligands were scored using Openeye Docking’s Chemgauss4 scoring function and the minimum score for each ligand was selected for rank ordering.

Answer 1

No

Answer 2

No