About VF-Unity usage

#1

Hello,
I am not sure whether it is the correct place to ask questions about VF-Unity since I did not find tags related with it. If not, please remove the question.

The first example in the github involves docking a single ligand using run_vf_unity.py The output folder contains 16 poses. What parameter in config.txt to change If I want to change the number of poses produced. In docking_output.csv, there are 9 scores for each pose such as
0.pdbqt,"-9.7,-9.6,-9.3,-9.1,-9.1,-9.0,-8.9,-8.9,-8.8",./outputs/pose_0.pdbqt
Are these 9 scores for 9 docking for each pose?

The second example involves docking multiple ligands. The docking results are multiple output folders (with name outputs_index), each corresponds with an input ligand and each containing several poses. Are they arranged according to docking scores? There is also an output folder containing poses just for one of the ligands. Is this ligand best for this protein? If I want to do a virtual screening for millions compounds, can VFU simply provide best 100 ligands according to docking score, each with one best pose?

Thanks for help !

#2

I have exactly the same question.
Does anyone have an insight on this?

Thank you!

#3

Hi xiy127,

I do not have any direct experience with VF-Unity, but the parameter that you are most likely looking for (in the config.txt file) is num_modes = 1
If it is not defined explicitly in the config file, than it assumes the default value (=9). What it does is set the maximum number of binding modes to generate.

You can also open each .pdbqt file that was generated by the docking and you will find a line that indicates the docking score.

Hope this helps!

Best,

Sorin