r27n0-LigandScoringProtocol.txt

Name

min_cross

Software

Smina Feb 28 2016, based on AutoDock Vina 1.1.2
Openbabel 2.3.2
Pymol 1.8.4.2
Python 2.7.11
Matplotlib 1.5.1
Scipy 0.17.0
Click 6.6

Parameters

Default parameters used for all programs.

Method

Based on predicted poses, compounds were minimized in the CatS_8 receptor using Smina and were then ranked by best Smina score.

Answer 1

No

r27n0-PosePredictionProtocol.txt

Name

min_cross

Software

Smina Feb 28 2016, based on AutoDock Vina 1.1.2
Openbabel 2.3.2
Pymol 1.8.4.2
Omega2 2.5.1.4
Python 2.7.11
Matplotlib 1.5.1
Scipy 0.17.0
Click 6.6
Open3dAlign

System Preparation Parameters

Default parameters used for most programs. Compounds protonated using -p flag with Openbabel.

System Preparation Method

Publically available holo structures of CatS were obtained from the pdb and then aligned to the CatS S04- structure provided in Pymol using only conserved secondary structure regions. Compounds were converted from SMILES strings to 3D sdf files and protonated using Openbabel.

Pose Prediction Parameters

Default parameters

Pose Prediction Method

Conformers were generated from SMILES strings using Omega2 and were then aligned to the most chemically similar ligand in available co-crystals using Open3dAlign.

Answer 1

No

Answer 2

Yes