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.
Compounds were converted from SMILES strings to 3D sdf files and protonated using Openbabel.
Smina docking generated 20 poses (--num_modes 20).
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.
Yes
Yes