align_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.
Based on predicted poses, compounds were minimized in the most similar receptor using Smina and were then ranked by best Smina score.
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
Open3dAlign
Default parameters used for most programs. Compounds protonated using -p flag with Openbabel.
Publically available holo structures of CatS were obtained from the pdb and then aligned to the CatS S04- structure provided in Pymol using only conserved secondary structure regions. Compounds were converted from SMILES strings to 3D sdf files and protonated using Openbabel.
Default parameters
Conformers were generated from SMILES strings using Omega2 and were then aligned to the most chemically ligand of available co-crystals using Open3dAlign.
No
Yes