tjwks-PosePredictionProtocol.txt

Name

D3R-GC3-Pose-Best-RMSD

Software

CACTVS Chemoinformatics Toolkit v3.433/Schrödinger Suite 2016-1/CORINA v3.60/UCSF Chimera v1.10.2/GOLD v5.2

System Preparation Parameters

Protonation state of ligands at pH 7.0+/-1 was considered.

System Preparation Method

All proteins were superimposed onto the reference SO4-bound structure using UCSF Chimera, so that all docking calculations can be carried out in a coordinates system compatible with the submission. Protein was 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+/-1 were generated using Schrödinger LigPrep. Binding site was defined as a sphere with 20 Å radius around a virtual point with coordinates (-7,12,-8).

Pose Prediction Parameters

Gold software with ASP 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 scoring function, and default values except search efficiency which was set to 200%. Ligands CatS_4 and CatS_6 were docked onto the 3MPF structure, CatS_14 onto the provided CatS_DMSO_structure_D3R_GC3 structure, CatS_2, CatS_17, CatS_20, CatS_22, CatS_23, CatS_24 onto the provided CatS_SO4_structure_D3R_GC3 structure, and the rest of ligands onto the 1GLO structure. The two flip/flop forms of the amide side chain from Asn161 were considered, and then best pose selected. The RMSD between the common substructure of the ligand and of one of PDB ligands 599, 23Z and N2A was calculated using an in house developed script based on CACTVS Chemoinformatics Toolkit. The score of poses with the best RMSD were selected for submission (1 score 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