htav7-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

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

Each compound was docked to the corresponding receptor structure with docking box defined by the publically available cocrystal ligand most similar to it. The best pose or poses were then selected by hand from highest scored poses. Alternate poses were generated by aligning compounds to target ligand and generating conformers using Openbabel. Conformers were then minimized in corresponding receptor.

Answer 1

Yes

Answer 2

Yes