1147-1-t4dmy-CatS_pose_prediction.txt

Name

Lead Finder template docking

Software

Build Model/xedconvert/Lead Finder

System Preparation Parameters

Assumed pH 5.4

System Preparation Method

Model was prepared using BuildModel and pH 5.4 with default parameters.
Ligands were prepared using xedconvert tool, and aligned to 3iej reference ligand. Key water molecule was retained during docking.

Pose Prediction Parameters

Template docking
10 independent docking runs

Pose Prediction Method

Ligands were and docked with Lead Finder using template
docking feature. 10 independent docking runs were performed. Docking results were
filtered. Only poses with h-bond to a key water molecule and Val192 were retained,
of those the pose with best dG as predicted by Lead Finder was taken.

Answer 1

Yes

1147-2-secjh-CatS_scoring_limited.txt

Name

Lead Finder reparametrized on a limited dataset

Software

Lead Finder

Parameters

default

Method

CatS ligands from ChemBl with experimental values of dG + CatS ligands
from D3R 2017 challenge were used. Ligands which are similar to available CatS
ligands from PDB were docked into most similar protein structure. Best poses
were identified, and Lead Finder energy components together with structural
descriptors of ligands and their poses were used to parametrize scoring function.

Answer 1

Yes