Foldit Drug Design Blog: Interface Update

Hi folks,

It's time for another update on the process we have been using to update the graphics for Foldit drug design!

This project started awhile ago with a very simple interface.

The idea that we had was to use the graphical user interface for designing proteins. In the image above, you see that we have a pi-menu pop up when you select an atom to design. While this is a pretty cool concept, the main problem that we encountered was that the pi-menu hid the ligand that you were supposed to be designing. It was very difficult to perform modifications and see how it effected the protein/ligand.

This difficulty resulted in a move to a separate menu.

In this menu, which we call the Ligand Design Panel, you can select atoms to design and then click on the design panel to change those atoms. The cool thing is now you can move the design panel around and view the protein and the ligand without interference with the menu. There are of course, some problems with this menu. We have some mixed opinions on this, and invite you to share your thoughts in our thread below.

The elements that you can choose from are just labeled with the element name: C-carbon, N-nitrogen, O-oxygen, P-phosphorus, etc. Also, the fragments shown below the elements, are kind of an ugly magenta. Further, when you click on an atom, then a fragment, you have no idea where that new fragment will be placed, spatially. So, we needed to update the ligand panel.

The new ligand panel is much more colorful! The elements are colored based on their CPK coloring and the fragments have been replaced with high-resolution images. Further, now, when you select a fragment, a glowing outline of that fragment is drawn onto the structure! No more guessing where a new fragment will be placed.

Additionally, we added the ability to modify bonds. Which brings us to the next graphical improvement. Before, everything was shown as a single bond. Now, the small molecule is drawn with its bonds shown and a new way of viewing the protein, called the Cartoon Ligand view option (under advance settings, View Protein: Cartoon Ligand) is available.

We have added new ways of viewing interactions within the protein.

We have also added a ligand viewing panel, which allows for turning the isosurface on only around the small molecule, showing areas where there are a hydrogen bond acceptor/donor, and finally, where there is repulsion between atoms. You can also change the transparency of everything on the fly, which allows you more direct manipulation of the settings.

Finally, we have added functionality that helps notify you if you are trying to design something that is not chemically feasible.

We hope everyone enjoys all the new additions. Let us know what other things you would like to see in the graphics department.

( Posted by  free_radical 83 1754  |  Tue, 03/24/2015 - 15:50  |  11 comments )
3
wisky's picture
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Squeeeeeeeeeeeeeeeeeeeeeee

*squeeeeeeeeeeee!!!!!!!!!!!!!!!!!*

I have been waiting for something like this forEVVVER. I like the new graphics where it shows double/triple bonds when necessary.

I am looking forward to when this gets used in a puzzle. :)

Good work!

Joined: 01/12/2015
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I am really excited too! We

I am really excited too! We are working hard to get this pushed out soon. Hopefully we can release a beta test soon (not used for rankings, just feedback)

sansyo's picture
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Is that possible to import

Is that possible to import pdb format ligand?

Joined: 01/12/2015
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We havent decided on any

We havent decided on any rules for the puzzles yet. There are some technical issues with loading a pdb format ligand into Foldit, but Ctab file format (.mol2, .sdf) might work.

twobob's picture
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file imports

Was there ever any motion on .sdf imports? or asnt's? pubchem does an xml format...

Joined: 08/30/2011
Love it

Can't wait to play. Are there already plans to go live?

Joined: 09/24/2012
Groups: Go Science
Thanks for the new chalenge !

Will there be a tutorial?

egran48's picture
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Tutorial and 'beginner puzzles'

Thank you, another steep learning curve. Can we please have a tutorial and maybe some smaller 'beginner type puzzles' to practice using the new tools before we get into the real work. :)

Joined: 01/12/2015
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fragmentor is working on

fragmentor is working on getting some tutorials going. We have decided on a beginner puzzle, already, but I dont want to give anything away :D

spvincent's picture
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Maybe this will become

Maybe this will become clearer when we've got something to play with but there seems to be an emphasis on building up a ligand atom by atom. While doubtless very flexible, it also seems potentially tedious and liable to result in chemically implausible structures. Might it not be easier to build up molecules from a library of functional groups? (ethyl, nitro, carboxyl, amide, etc., etc. ) I see what look like a few at the bottom of the panel but feel there should be a lot more.

Joined: 01/12/2015
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Hi spvincent, Right now is

Hi spvincent,

Right now is completely in a testing phase. Not shown in this blog post were some iterations of a separate panel I designed which contained 2D structures of fragments. The fragments that I had loaded in were based off of taking all the HIV protease inhibitors, scoring them with a QSAR model, fragmenting the drugs based on their scores, and displaying them in the panel with the QSAR score along with the fragment. I believe this is a powerful tool, but for now, we are interested in getting feedback on the simple interface.

Another thing not shown here is the ability to select multiple atoms and manipulate them all at a time. For example, in the benzene ring, you can select multiple atoms and then a single fragment and it will replace those atoms selected with the fragments. The same is true for selecting separate atoms.

I think that the possibilities are endless for the type of interfaces we can cook up. I like the suggestions and I am more than willing to try and get more things that everyone wants in the game!

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons