1146-1-7uhs4-aligned_Vina_PoseProtocol.txt

Name

Aligned 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, PDB lig name, and SMARTS pattern of the MCS for each BACE ligand.
1 conformer was generated with rdconf.py.
The aligned pose was generated via obfit to align the conformer to the MCS via the SMARTS pattern from above

Pose Prediction Parameters

score_only #flag to just compute the score of the provided pose

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).
The top 1 poses are submitted with this protocol.
The commands to run this protocol are given in the provided aligned_vina_jobs.txt file.

Answer 1

No

Answer 2

Yes

1146-2-my2ui-aligned_Vina_LigandScoringProtocol.txt

Name

Aligned Autodock Vina

Software

rdkit/gnina/smina

Parameters

score_only #flag to just compute the score of the provided pose

Method

Docking was performed using smina (a fork of Autodock Vina) via the gnina software package with the above parameters (defaults for the rest).
The top 1 poses are submitted with this protocol, as selected by the best Affinity from Vina
The commands to run this protocol are given in the provided aligned_vina_jobs.txt file.

Answer 1

No

Answer 2

No