1146-1-orpqh-PosePredictionProtocol.txt

Name

Lead Finder + reduced xedex conformer sampling

Software

Lead Finder 1808, xedex, Build Model 1808

System Preparation Parameters

Ligands 3D optimized using xedmin tool
Rings conformations generated using xedex, (-D 50 -m 20)

System Preparation Method

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 -m 20 option). All aliphatic NH were manually protonated to (+) state,
amide bonds in cyclic rings were set to trans- conformation. 3 protein models were used for docking

Pose Prediction Parameters

10 independent docking runs / model + ligand + conformation
default docking parameters

Pose Prediction Method

10 independent docking runs of Lead Finder 1808 with default parameters were used per
conformation per model. H-bonds filters were applied to poses: h-bonds with residue 230, and (residue 32
or residue 228. Filtered poses were sorted by Lead Finder dG, and poses within 1 kcal/mol of minimum were
inspected and rated (A = best, B = some H-bonds missing, C = many H-bonds missing, D = incorrect). Pose with
the lowest dG of the highest rate were selected for each ligand. Ligands, for which no poses satisfying
hbonds and dg filters were reviewed and rated manually, and same procedure was applied.

Answer 1

Yes

1146-2-zv330-LigandScoringProtocol_othd.txt

Name

Lead Finder over-the-hood docking

Software

Lead Finder 1808

Parameters

default Lead Finder parameters

Method

Standard Lead Finder dGs were calculated for poses and over-the-hood docking protocol was
applied. Ligands were docked at 20 random surface patches of 3dv5 (2 times in each patch). For
each ligand/patch maximum dG was used. Then for median over surface patches was used as othd energy
of the ligand. Resulting score is dG - othd.

Answer 1

Yes