Identify unsatisfied polars in H-bonds

Case number:845833-2012329
Topic:Game: Display
Opened by:BootsMcGraw
Opened on:Monday, November 15, 2021 - 05:40
Last modified:Wednesday, November 24, 2021 - 10:23

I've got a beautiful network in puzzle 2070: twelve interface bonds. But I'm getting only 2100 points for it, because only 87.5% of the polar atoms are satisfied.

Honestly, I can't see where I have any unsatisfied polars in my network. I ask that the game dev's please implement a function that shows unsatisfied polars in an H-bond network, much like we can see BUNS by checking a box in the Objectives. I can't fix what I can't see.

(Mon, 11/15/2021 - 05:40  |  5 comments)

bkoep's picture
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Joined: 11/15/2012
Groups: Foldit Staff

Yes, that's a good point! We should be able to highlight unsatisfied atoms.

Can you also share this solution so I can make sure there's not a bug in the existing behavior? BUNS atoms are tricky to count...

Joined: 12/06/2008
Groups: Contenders

Solution shared with scientists "82314-2070".

I have an asparagine at residue 16 that has a red bond from the oxygen to the network, so it is "scoring too low to be part of the network". Its nitrogen is bonded to nothing. Could this be the cause?

Funny, removing ASN 16 drops my network score from 2100 to 1800, so I fail to see how it's not part of the network. Conflicting observations.

HuubR's picture
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Joined: 04/13/2020
Groups: Gargleblasters

Just want to share my experience with red bonds and unsatisfied networks.

  • A red bond is not part of the HBN, but it does satisfy the polar atom on the residue that is part of the network. I think that could explain your drop from 2100 to 1800 when you remove the ASN and the red bond.
  • In case one of the blue bonds connects to the backbone, it seems that the sidechain of that residue, if it is hydrophilic, also needs to be fully satisfied (see note). In such a case, you can improve the score by replacing that residue by a hydrophobic one: then its sidechain no longer has polars that are counted as unsatisfied.

Note: I don't see the logic why the sidechain should be satisfied when the network only connects to the backbone. I would appreciate it when someone could explain that to me.

Joined: 03/28/2020
Groups: Go Science

Yes, this topic puzzled and sometimes puzzles me still as well. In my opinion this comes from the issue that a bipolar sidechain (serine, threonine or tyrosine) is used in your network. If you take a buried serine for example, it needs to make a bond from it's donor to an acceptor on the other end. But in addition, to the acceptor-part of the serine's atom the donor of another sidechain must be connected in order for the serine to count as fully-satisfied. The irritating thing is that the serine will not glow "red" (indicating an acceptor-bun) when it's donor has an hbond. Foldit-internal it will count as not fully satisfied though and will lead to decreased bonus.
In my opinion the hbnet scorefunction should be corrected so that any cross-Interface-core-bond that has a fully satisfied sidechain on each end of the bond (no matter how else the network looks like) will count as fully satisfied bond. 3 of those should give you full hbnet-bonus. As it is now, you will get decreased bonus if such a residue is only connected with it's donor anywhere to the net which can be frustrating. I try not to use these altogether due to this issue. I typically use a chain of 2 tryptophans (at the ends), 1 aspartate/glutamate and 1 histidine. These can in most cases be made to form a cross-interface chain which is fully satisfied and gives full bonus.

Joined: 03/28/2020
Groups: Go Science

On second thought, another nice way to fix this would be to change the hbnet-bonus-scorefunction so that serine, threonine and tyrosine would count as fully satisfied even if only their donor-part would have an hbond. Like this, there would be 4 (serine, threonine, tyrosine and Tryotophan) AAs which could be used as easy, single-polar terminators for open acceptor-atoms in a net (I would really have loved nature to give us something equivalent as only-single-acceptor but that would have been too easy ;o) ). Currently only tryptophan can do this and it is pretty bulky and therefore sometimes hard to place. This would probably greatly simplify the creation of deeply-buried, fully-satisfied nets and maybe increase their quality.
The resulting question that I have with this goes to scientists: are unsatisfied acceptors in buried serine/threonine/tyrosine an issue? Since they are currently not showing as buns I guess that they are not, so it would be great if the hbnet-bonus-scorefunction could be modified like proposed here.


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, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons