Blind docking with QVina-W

[mirix]

Hi,

It seems that if one wants to carry out blind docking with QVina-W still needs to supply the centre and dimensions of the search box, is that correct?

Best,

Miro

[aalhossary]

Hi Miro,
Yes it is still needed. Actually QVina-W just modifies QVina (and Vina) search method.
However, yours is a good point.
In the time being, we can supply a small BASH script to calculate it for you. and we may include that automatically in a subsequent version.
@Roses-Roses May you upload a script to do that, please?

[kabirbiswas]

"In the time being, we can supply a small BASH script to calculate it for you. and we may include that automatically in a subsequent version." - would be nice to have a script to automatically create a grid box.
Thanks.

[mirix]

Hi again,

Any news regarding this question?

Best,

Miro

[kabirbiswas]

No, not yet.

[mirix]

Other suggestions:

1. Ability to work with multiconformer SDF files. Vina can handle rotamers but not macrocycles.

2. Ability to handle protein ensembles.

3. Integration with OpenBabel to handle other chemical formats in addition to PDBQT.

Smina can already do 1 and 3 but QVina is much faster and Smina do not have the blind docking capabilities of QVina-W.

[Rohit-Satyam]

Is there any update. Actually I was planning using Qvina-w. However, it seems it still requires to input search space parameters. Does anyone have a shell script @aalhossary discussed?

[aalhossary]

Is there any update. Actually I was planning using Qvina-w. However, it seems it still requires to input search space parameters. Does anyone have a shell script @aalhossary discussed?

• I am very busy with other issues.
• QuickVina-W takes the same parameters as Vina, described here
  http://vina.scripps.edu/manual.html#usage
• The input search space can be generated graphically using the tool shown here (please make sure that the spacing is set to 1 angstrom)
  http://vina.scripps.edu/tutorial.html
• I hope I can find time to write a script over the weekend

[aalhossary]

Other suggestions:

1. Ability to work with multiconformer SDF files. Vina can handle rotamers but not macrocycles.
2. Ability to handle protein ensembles.
3. Integration with OpenBabel to handle other chemical formats in addition to PDBQT.

Smina can already do 1 and 3 but QVina is much faster and Smina do not have the blind docking capabilities of QVina-W.

Thanks for suggestions. However, I don't think I will have chance to do them any soon

[mirix]

There is a chunk in following Python script to find the centre and the dimensions of the protein and feed them to QVina-W:

https://gitlab.com/miromoman/drepy

Scroll to the docking section.

I have a similar Bash script but I will need some time to find it.

[o7o]

Thanks mirix for yours