1146-1-pngm0-Blind_Vina_PoseProtocol.txt

Name

Blind Autodock Vina

Software

rdkit/gnina/smina

System Preparation Parameters

Assumed pH to be 7.4

System Preparation Method

I used RDkit to determine which ligand in Pocketome was closest to a given smile via the rdFMCS function to find the maximum common substructure (MCS).
This was determined by counting the number of bonds in the MCS and storing which ligand had the most.
This was done with the provided smile_comp.py script, and accompanying comp_jobs & bace_lig_smiles.txt files.
The output of the script gives the PDB id, and PDB lig name of the MCS for each BACE ligand

Pose Prediction Parameters

exhaustiveness=8 #default value for exhaustiveness of search
autobox_add=20 #number of angstroms to add to the search space generated by autobox (default 4)
num_modes=10 #maximum number of modes to generate from the search (default 9)

Pose Prediction Method

Docking was performed using smina (a fork of Autodock Vina) via the gnina software package with the above parameters (defaults for the rest), and an autobox that was generated from the MCS found in the previous setps.
The top 5 poses are submitted with this protocol.
The commands to run this protocol are given in the provided blind_vina_jobs.txt file.

Answer 1

No

Answer 2

Yes

1146-2-rjj7d-Blind_Vina_ScoreProtocol.txt

Name

Blind Autodock Vina

Software

rdkit/gnina/smina

Parameters

exhaustiveness=8 #default value for exhaustiveness of search
autobox_add=20 #number of angstroms to add to the search space generated by autobox (default 4)
num_modes=10 #maximum number of modes to generate from the search (default 9)

Method

Docking was performed using smina (a fork of Autodock Vina) via the gnina software package with the above parameters (defaults for the rest), and an autobox that was generated from the MCS found in the previous setps.
The minimizedAffinity (result from AutoDock Vina) was used to sort the molecules and taken as the Score
The commands to run this protocol are given in the provided blind_vina_jobs.txt file.

Answer 1

No

Answer 2

No