1147-1-yfvnb-PosePredictionProtocol.txt

Name

D3R-GC4-Score-Phase-2-PosePredictionProtocol-BestScore

Software

CACTVS Chemoinformatics Toolkit v3.433/Schrödinger Suite 2018-1/CORINA v3.60/UCSF Chimera v1.10.2/GOLD v5.2

System Preparation Parameters

Protonation state of ligands at pH 7.0 was considered.

System Preparation Method

The PDB structure 1GLO was superimposed onto the reference structure from D3R GC3, then prepared (hydrogens added) using the Hermes graphical interface of GOLD software. 3D coordinates of the ligands (MOL2 format) with different protonation states corresponding to a pH of 7.0 were generated using Schrödinger LigPrep. Binding site was defined as a sphere with 20 Å radius around a virtual point with coordinates (-7,8,-4).

Pose Prediction Parameters

Gold software with ASP (the Astex Statistical Potential) scoring function
Search efficiency 200% # more adapted for flexible ligands
100 poses generated for each ligand

Pose Prediction Method

Docking runs were executed using Gold and ASP (the Astex Statistical Potential) scoring function, and default values except search efficiency which was set to 200%. To explore ring conformations and the ligand flexibility the options flip ring corners, flip pyramidal N and flip amide bonds were activated. All the ligands were docked onto the 1GLO structure prepared as stated above. The docking calculations were carried out without any constraints on the protein or the ligands.
The poses with the best docking score were selected for submission (1 pose per compound).
Protein structures were converted into PDB format for submission using UCSF Chimera, and the docking poses were converted into MOL format using CORINA (the MOL format corresponds to the SDF output format in CORINA).

Answer 1

No

Answer 2

No

1147-2-6hih0-LigandScoringProtocol.txt

Name

D3R-GC4-Score-Phase-2-LigandScoringProtocol-BestScore

Software

CACTVS Chemoinformatics Toolkit v3.433/Schrödinger Suite 2018-1/CORINA v3.60/UCSF Chimera v1.10.2/GOLD v5.2

Parameters

Protonation state of ligands at pH 7.0 was considered.

Method

Docking runs were executed using Gold and ASP (the Astex Statistical Potential) scoring function, and default values except search efficiency which was set to 200%. To explore ring conformations and the ligand flexibility the options flip ring corners, flip pyramidal N and flip amide bonds were activated. All the ligands were docked onto the 1GLO structure superimposed onto the reference structure from D3R GC3. The docking calculations were carried out without any constraints on the protein or the ligands.
The poses with the best docking score were selected for submission (1 pose per compound).

Answer 1

No

Answer 2

No