Lead Finder template docking
Build Model/xedconvert/Lead Finder
Assumed pH 5.4
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.
Template docking
10 independent docking runs
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.
Yes
Lead Finder reparametrized on a limited dataset
Lead Finder
default
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.
Yes