1146-1-yoc36-PosePredictionProtocol_pose_flexible_alignment.txt

Name

Ligand_shape_similarity_flexible_alignment

Software

AutoDock Vina 1.1.2/RDKit 2018.03.1/Openbabel/Pymol/fkcombu

System Preparation Parameters

Default parameters used for most programs.

System Preparation Method

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 assign charges and atomtypes to ligand as PDBQT files.
MGLTools was used to generate PDBQT files for receptor protein.

Pose Prediction Parameters

Vina docking with local_only mode
Vina scoring funtion (empirical + knowledge-based function)

Pose Prediction Method

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 RDKit.
The most similar ligand and its corresponding protein structure A was used as template.
The 20 target compounds were flexibly aligned and superimposed by fkcombu software with the most similar ligand as template.
The target compound was docked into protein A using AutoDock Vina with local_only mode to avoid possibility of wrong pose.

Answer 1

Yes