dock_close
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 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. Compounds were then ranked by predicted smina value.
No
align_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 VEGFR2 were obtained. Compounds were converted from SMILES strings to 3D sdf files and protonated using Openbabel.
Default parameters. 30 conformers generated using Omega.
For each test compound, the available cocrystal ligand with the highest chemical similarity was calculated.
Each compound was then aligned to the corresponding ligand and minimized in that receptor.
No
Yes