Flexible docking using gwovina

#1

Hi Christoph,

Firstly, this is an excellent project that brings high throughput virtual screening within reach of those of us who are classically trained wet lab biologists. So for that, I thank you. I also believe that making the Enamine REAL libraries widely available in docking-ready format is extremely valuable, and would hope that VirtualFlow can continue to expand with with the REAL library. Again, thank you for this valuable work you have done.

Now on to the question at hand:

I’ve performed a 1.1B compound rigid receptor screen using VF1 (My home cluster runs an LSF, VF2 does not have a LSF template currently). I’m now interested in running a secondary screen with flexible residues in the receptor, using gwovina for the reduced computational cost. I’ve generated flexible.pdbqt (containing only the flexible residues) and rigid.pdbqt (containing the entire receptor) files using AutoDock Tools. So finally, actually to the question:

  1. How does one input the rigid.pdbqt file and the flexible.pdbqt into Virtualflow using gwovina? Is it through the config file? If so, what is the syntax for that type of entry?

Second bonus question:

  1. Does the gwovina module work with VF1?

Thanks again,

Best,

Kris White

#2

Hi Kris and welcome to the forum!

I do not have direct wxperience with gwovina, but considering it is actually a vina fork, one should be able to define the flexible residues in the same way, namely by using the --flex flag followed by your flexibile residues pdbqt file:

qwovina --config conf.txt --receptor rigid.pdbqt --flex flexible.pdbqt

you can use the same flag inside your config.txt file to point to the flexible.pdbqt file

Hope this helps!

Kind regards,

Sorin