LeadFinder dG score on ensemble
LeadFinder v 1708
delta G score
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.
LeadFinder template docking with filters
LeadFinder/BuildModel
Assumed pH 5
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.
Template docking mode
Number of independent runs=10 #Two independent docking runs for each combination of ligand/model
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.
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