hnjio-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

For each compound generated pose was scored by smina and used to rank.

Answer 1

No

hnjio-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

System Preparation Parameters

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

System Preparation Method

Publically available holo structures of JAK2 were obtained from the pdb. Compounds were converted from SMILES strings to 3D sdf files and protonated using Openbabel.

Pose Prediction Parameters

30 conformers generated using Omega2.

Pose Prediction Method

For each test compound, the available cocrystal ligand with the highest chemical similarity was calculated.
Conformers for each compound were then generated using Omega2 and aligned to the closest ligand using open3dalign. Each compound was then
minimized in the receptor of pdbid 1Y6A.

Answer 1

No

Answer 2

Yes