SHAFTS_LeDock_docking
LeDock/LePro/RDKit 2018.03.1/Openbabel/Pymol/SHAFTS(Cynthia)
Default parameters used for most programs.
1000 conformers were generated for each target compound using genConf.py script.
3D structure of target compounds was generated using RDKit from smiles.
Hydrogen was added and conformation was generated with ETKDG method in RDKit.
Openbabel was used to convert file formats.
Receptor structure was prepared by LePro.
Default parameters used for most programs.
Publically available structures of Beta-secretase 1 from pdb database was obtained.
The ligands were extracted and compared with target compound using Maximum Common Substructure method in RKDit.
11 most similar ligands were found.
1000 conformers were generated for each target compound using genConf.py script.
All conformers were compared to the 11 template ligands using SHAFTS(Cynthia) programme based on 3D molecular similarity calculation,
and the conformer of target compound with the highest similarity score was kept and superimposed on corresponding receptor structure.
The target compound was docked into the receptor using LeDock to generate at most 20 poses. The best pose was chosen manually and submitted.
Yes