Lead Finder + xedex conformer sampling
Lead Finder 1808, xedex, Build Model 1808
Ligands 3D optimized using xedmin tool
Ligands protonated at pH 7.4
Rings conformations generated using xedex (-v 50)
Build Model 1808 with default settings was used for preparation of protein models.
Ligands were converted to 2D using babel, 3D optimized using xedmin tool. Ligand macrocycle conformations were
sampled using xedex tool (with -D 50 option). All aliphatic NH were manually protonated to (+) state,
amide bonds in cyclic rings were set to trans- conformation. Several most appropriate protein models per
ligand were selected for docking.
3 independent docking runs / model + ligand + conformation
default docking parameters
3 independent docking runs of Lead Finder 1808 with default parameters were used per
conformation per model. Results were clusterized using DBSCAN algorithm (eps=0.5, m=5). For each cluster the pose
with the best dG was selected. Only poses satisfying H-bonds filters: h-bonds with residue 230, and (residue 32
or residue 228) were considered. Poses satisfying filters were manually reviewed and selected for submission.
Yes
No