LeadFinder template docking
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. In
the model based on 3IEJ, different protonation states of Glu115 were sampled, and at
the place of Asn161 were Asn, Ala and Asp. Ligand 3D conformations were generated
using ACD/Labs ChemSketch. 24 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=2 #Two independent docking runs for each combination of ligand/model
LeadFinder dG scoring function (empirical function)
Docking runs were executed with the above specified parameters while default values
were applied for the rest of the variables. Poses were manually inspected and rated; poses with highest rating
from different models and runs were pooled, pose with the best dG was selected.
Yes