display information at atom level for ligands

Case number:845833-2005209
Topic:Game: Display
Opened by:LociOiling
Status:Open
Type:Suggestion
Opened on:Saturday, May 12, 2018 - 19:18
Last modified:Tuesday, May 15, 2018 - 02:29

For proteins, the chemical structure of each amino acid is known. A recipe can report most of the key features, for example Atom Tables 1.21.

For drug design puzzles, the goal is to create a new ligand with unique chemistry. View options, including "Ligand Specific" coloring and "Cartoon Ligand" protein view can help reveal the structure of the ligand.

There's been a longstanding request for a Lua function structure.GetAtom to return atom types, which would allow recipes to "see" ligands better.

While Ligand Specific and Cartoon Ligand are helpful, the CPK coloring they use is somewhat obscured when the ligand is selected. It can be hard to distinguish the yellow of sulfur from the yellow-green of fluorine. Phosphorus is about the same color as frozen backbone, and doesn't have a lot of contrast with hydrogen. With the ligand selected, phosphorus with two attached hydrogens looks like valine.

These problems are compounded for those with limited color vision.

It would be helpful for Foldit to reveal the atomic makeup of proteins and ligands in the GUI. Molecule viewers such as JMol have this feature. Hovering over a protein atom displays the residue code and sequence number, the atom type and position in the residue, and the atom number in the overall model. Hovering over a ligand atom displays the ligand code, the atom name in the model (including the element), and the atom number in the model.

Foldit already has a similar function for bondable atoms, which displays acceptor, donor, or donor/acceptor when you hover over an atom with "show bondable atoms" selected. It seems like this function could be extended for all atoms, displaying basic information and including the bonding information when it applies.

JMol atom display for proteinJMol atom display for protein
JMol atom display for ligandJMol atom display for ligand

(Sat, 05/12/2018 - 19:18  |  3 comments)


spvincent's picture
User offline. Last seen 46 min 29 sec ago. Offline
Joined: 12/07/2007
Groups: Contenders

I agree that ligand visualization needs more work. I have a hard time seeing what the structure looks like and modifying it is somewhat hit and miss for me with the current tools. For example, if I add an oxygen somewhere, what is being made? An alcohol? A ketone? An ether? Something else?

Joined: 05/19/2017
Groups: None

As a chemistry buff even I have trouble getting functional groups right every single time. The game could definitely have the potential to have a crash course in this, but until then, I totally get where you're coming from. Personally, I'm going into a field with a lot of organic chemistry involved, and yet I still find it difficult to take it all in and retain knowledge.

Joined: 09/22/2017
Groups: Beta Folders

If it's of any value to anybody you can print this guide to simple oxygen functional groups

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