grhvk-FreeEnergyProtocol.txt

Name

quasi-exact

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

Parameter

Default parameters were used for each software.

Method

For each test compound, the available cocrystal ligand with the highest chemical similarity was calculated.
Each compound was then docked to the corresponding receptor structure with docking box defined by the cocrystal ligand. The best pose or poses were then selected by hand from highest scored poses. The quasi-exact method as described in https://doi.org/10.1093/bioinformatics/btp664 was then applied to each compound to calculate free energy of binding.

Answer 1

Yes

grhvk-PosePredictionProtocol.txt

Name

dock_close

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

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

Smina docking generated 20 poses (--num_modes 20).

Pose Prediction Method

For each test compound, the available cocrystal ligand with the highest chemical similarity was calculated.
Each compound was then docked to the corresponding receptor structure with docking box defined by the cocrystal ligand. The best pose or poses were then selected by hand from highest scored poses.

Answer 1

Yes

Answer 2

Yes