IVS in PyRx

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IVS in PyRx

Postby wrmartin » Mon Jun 15, 2015 11:19 pm

Hello Sargis,

Another user asked about inverse virtual screening, but I thought a new thread on the topic would be better as it wasn't the main point of the thread. I've tried a few other programs to do IVS, but their requirements make them cumbersome in some way, or are not user friendly. It seems to me you could pretty easily implement IVS (programming notwithstanding) with the groundwork you've already laid.

Since you've already implemented a way to determine ligands in the protein when it is added, it seems you would only need to use this identification to create .pdbqt files without these ligands for the initial "prep", as PyRx already does with user prompts, but automatically. For instance, for a protein with two ligands [xxx] and [yyy]. creating files protein.xxx.pdbqt and protein.yyy.pdbqt. Possibly a user-inputable list of common cofactors, or a built-in list? Built-in sounds like a lot of extra work for you. Personally, it would be fine to just ignore the results which docked where the cofactor goes.

As for the search area, maybe a user-inputted distance from the deleted ligand? A 5 angstrom input would mean a search space at minimum 5 angstroms from any atom in the ligand. I don't know if PyRx already can determine the coordinates of atoms, but if it can, forming the box should be easy (biggest/smallest in each direction, add/subtract inputted value respectively).

I *think* everything else is already implemented. Your work on this software is appreciated!
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Re: IVS in PyRx

Postby sargis » Tue Jun 16, 2015 2:11 am

Thank you for the message. I've started implementing inverse virtual screening and would be glad to hear your feedback on this. I'm almost done with molecules selection page. It would be similar to what's already implemented, expect that users can now select multiple macromolecules. Implementing user interface for the search area is a bit tricky. I'm thinking to load all the macromolecules and having a drop-down menu above the search space parameters so that users can select different macromolecules and adjust search space for each macromolecule as needed. By default, this search space will include the whole macromolecule (blind IVS?).

Now I'm at the point where I need to program so that the bounding box for the search space will be updated depending on which macromolecule the user selects from the drop-down list.

I appreciate your feedback and thank you for using PyRx!
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Re: IVS in PyRx

Postby wrmartin » Tue Jun 16, 2015 2:21 am

I'd definitely love to take a look. I don't know how you do your builds, but if you have a "beta" I could take a look at I would love to do so. The other solutions I've found for IVS either use a less rigorous method for screening or require grid files for each protein, which really defeats the purpose with more than a few proteins.
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Re: IVS in PyRx

Postby sargis » Mon Nov 02, 2015 12:26 am

wrmartin wrote:I'd definitely love to take a look. I don't know how you do your builds, but if you have a "beta" I could take a look at I would love to do so. The other solutions I've found for IVS either use a less rigorous method for screening or require grid files for each protein, which really defeats the purpose with more than a few proteins.

I just uploaded a new updates that implements IVS in PyRx. Please use PyRx > Help > Check for Updates... menu to apply this update.

With this update you'll be able to select multiple Macromolecules using Ctrl or Shift key similar to when selecting multiple Ligands. Please give it a try and let me know what do you think.

Thank you for using PyRx!
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Re: IVS in PyRx

Postby wrmartin » Mon Nov 02, 2015 4:38 pm

I updated, and while it lets me select multiple macromolecules, it says there are no macromolecules selected and will not allow me to move on to the next step in the vina wizard. The autodock wizard does the same.
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Re: IVS in PyRx

Postby sargis » Mon Nov 02, 2015 4:57 pm

wrmartin wrote:I updated, and while it lets me select multiple macromolecules, it says there are no macromolecules selected and will not allow me to move on to the next step in the vina wizard. The autodock wizard does the same.

Strange, this works for me. There might be no pdbqt files in the macromolecules folder or something else was selected under Macromolecules. Would it be possible to take a screenshot similar to the one shown below? Thank you.
ivs_pyrx.png
ivs_pyrx.png (91.35 KiB) Viewed 4249 times
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Re: IVS in PyRx

Postby wrmartin » Mon Nov 02, 2015 5:07 pm

2015-11-02 (1).png
2015-11-02 (1).png (96.33 KiB) Viewed 4249 times

2015-11-02 (2).png
2015-11-02 (2).png (96.56 KiB) Viewed 4249 times

2015-11-02 (3).png
2015-11-02 (3).png (95.01 KiB) Viewed 4249 times


I can't get to the screen you have displayed.
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Re: IVS in PyRx

Postby sargis » Tue Nov 03, 2015 3:16 am

Thanks you, that's very helpful. I'm able to reproduce this if I select 2 macromolecules, then right-click and Refresh. I can see 2 macromolecules selected if I select one and then Ctrl-click another. I'll try to fix this and upload another update...
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Re: IVS in PyRx

Postby sargis » Wed Nov 04, 2015 1:45 am

I've uploaded another update that keeps track of selected macromolecules when doing right-click and Refresh. This works for me on Windows 7.

I'm planning to upgrade 3rd party libraries in one of the future releases of PyRx that might fix this issue if multiple molecule selection. Please try this new update and let me know if it works. Thank you.
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Re: IVS in PyRx

Postby wrmartin » Mon Dec 07, 2015 3:31 pm

I received your PM, but cannot reply since you have PMs disabled. I am fully updated, and while it will allow me to select multiple macromolecules, I cannot proceed with them selected. The screenshots are still accurate. I am using Windows 10, if that is possibly an issue.
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