min-cross
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
Default parameters used for all programs.
For each compound generated pose was scored by smina and used to rank.
No
dock_close
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
Default parameters used for most programs. Compounds protonated using -p flag with Openbabel.
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.
30 conformers generated using Omega2.
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 5TQ3.
No
Yes