free_radical Lv 1
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.
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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.
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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.
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We have added new ways of <a href-"https://www.youtube.com/watch?v=smo27Z2hyPk">viewing interactions within the protein</a>.
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.
