w6bwq-LigandScoringProtocol.txt

Name

LeadFinder dG score on ensemble

Software

LeadFinder v 1708

Parameters

delta G score

Method

For all poses which passed structural filters as described in the pose preparation
protocol we calculated dG score as reported by LeadFinder. We then reported a median over
a set of all dGs for ligand.

w6bwq-PosePredictionProtocol.txt

Name

LeadFinder template docking with filters

Software

LeadFinder/BuildModel

System Preparation Parameters

Assumed pH 5

System Preparation Method

BuildModel with default parameters and manual adjustment.
Protein models were prepared using default BuildModel algorithm at pH 5. Key water
molecule was retained, other water molecules were discarded during protonation. Ligand 3D
conformations were generated using ACD/Labs ChemSketch. 136 ligands were aligned with
reference ligands from protein models using falign tool from Cresset, and were used
as a starting points for template docking using leadfinder. The grid box was determined
using default LeadFinder algorithm and reference ligands to determine box size.

Pose Prediction Parameters

Template docking mode
Number of independent runs=10 #Two independent docking runs for each combination of ligand/model

Pose Prediction Method

Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. Two structural filters were used: hydrogen bond between
ligand and key water molecule, and contact between position of CF3 group and ligand. Poses passing the
filter were selected for dG calculations.

Answer 1

No