1470-1-zqf0m-PosePredictionProtocol.txt

Name

Flexible-ligand docking protocol using RDkit generated low energy conformers

Software

Smina (A fork of Autodock Vina)/ RDKit (Version 2018.03.2)/ PDB2PQR (Version 2.1.1)/ AutoDockTools (Version 1.5.6)

System Preparation Parameters

Assumed pH 4.5
Gasteiger charges

System Preparation Method

1. Receptor selection for docking:
20 given receptors from D3R Challenge were used for self-docking.

2. Receptor preparation: PDB2PQR was used to add hydrogens to the receptor structures (—-ph_calc-method=propka —with-ph=4.5),
AutoDockTools was used to convert the input receptors files to pdbqt format and assign Gasteiger charges (All the waters were retained).

3. Ligand conformation selection for docking:
Ligand conformational libraries were generated using RDkit (maximum 1000 conformers per ligand, ETKDG method).
Ligand conformers within 5 kcal/mol from the lowest energy were selected for docking. (Energy calculation of ligand conformers using MMFF94)

Pose Prediction Parameters

Ligands were treated as flexible, receptor structures were treated as rigid.
The docking box site were determined by the known crystal ligands. (Known crystal ligand is used for autobox)
Exhaustiveness=32
Num_modes=20
Energy_range=7
Standard Vina scoring function

Pose Prediction Method

Docking runs were executed with the above specified parameters while default values were applied for the rest of the variables. The top 1 pose from the Smina docking are submitted with this protocol.

Answer 1

No

Answer 2

Yes