puzzle picture
1995: Symmetric Trimer Design: H-bond Networks
Status: Closed

Summary

Name: 1995: Symmetric Trimer Design: H-bond Networks
Status: Closed
Created: 05/19/2021
Points: 100
Expired: 05/26/2021 - 23:00
Difficulty: Intermediate
Description: Design a symmetric protein trimer, with 3 identical chains of 60 residues each! This puzzle includes a Secondary Structure Objective, so no more than 50% of your design can form helices. The H-bond Network Objective encourages players to build buried, satisfied H-bond networks at the interface between symmetric chains. H-bond networks are a great way to introduce polar residues at the interface, but it's important that all of the bondable atoms make hydrogen bonds! We've also adjusted the H-bond Network Objective so that poor-scoring H-bonds may not contribute to networks; poor-scoring H-bonds will be displayed in red. This puzzle uses the Buried Unsats Objective, with a large penalty for buried polar atoms that can't make H-bonds. In this puzzle, there are no limits on the Complex Core, but we've included the Complex Core objective so players can see the core residues that can be incorporated into H-bond Networks.
Categories: Design, Overall, Symmetry

Top Groups

RankGroupScorePoints
1Contenders19,532100
2Gargleblasters19,02171
3Go Science19,01249
4Marvin's bunch19,00333
5Anthropic Dreams18,94922

Top Evolvers

Top Soloists



Need this puzzle? Log in to download.  

Comments

bkoep's picture
User offline. Last seen 1 day 6 hours ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Objectives

Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -150 points per atom (not including symmetric copies).

Core Existence: Monomer (max +1600)
Ensures that at least 16 residues are buried in the core of the monomer unit.

Core: Complex (max +0)
Awards no bonuses or penalties. Click Show to see which residues count as "Core" for the H-bond Network objective.

H-bond Network (max +1800)
Rewards networks that comprise at least 2 H-bonds involving core residues.
Between 1 and 9 H-bonds should cross the interface between symmetric units.
Networks must be at least 75% satisfied (i.e. 75% of all bondable atoms in a network must make a H-bond).

Interaction Energy (max +500)
Monitors that all large PHE, TYR, and TRP residues are scoring well.

SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, ALA in helices.

Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.

Secondary Structure (max +500)
No more than 50% of residues may form helices. Extra helices are penalized at 10 points per residue.

frood66's picture
User offline. Last seen 12 hours 8 min ago. Offline
Joined: 09/20/2011
Groups: Marvin's bunch
this crashes when mutating -

this crashes when mutating - no warning - just quits

frood66's picture
User offline. Last seen 12 hours 8 min ago. Offline
Joined: 09/20/2011
Groups: Marvin's bunch
not really playable - shame

not really playable - shame

milkshake's picture
User offline. Last seen 2 weeks 3 days ago. Offline
Joined: 07/17/2019
Groups: Foldit Staff
Hi frood, thanks for the

Hi frood, thanks for the report, it would help us if you could open up a solution where the crashing happens and use the "upload to scientists" feature. In the description box you could type some info about how to make it crash (for example, just click mutate and wait, or what-have-you.)

Thanks!

Bautho's picture
User offline. Last seen 1 week 6 days ago. Offline
Joined: 02/16/2012
Groups: Go Science
H-Bond network filter

I don't really understand the H-bond network filter.

In one example, I have 4 blue H-bonds in a row.
Serine-OH to Aspartate-O to Glutamine-NH to Aspartate-O to Arginine-NH
It says Interface HBonds: 3 (0 credited)
However, I only see two Glutamine-NHs from a neighboring protein have 2 bonds to two different Aspartate-Os.
All other residues are in one individual protein.

Polars Satisfied: 58.8235 %
I don't really understand how this odd number is calculated?
It would be more helpful if you could write something like "4 out of 13 possible atoms satisfied" into the filter

bkoep's picture
User offline. Last seen 1 day 6 hours ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Complicated

Yes, the H-Bond Network Objective is rather complicated, but that's because there are a lot of different aspects that make up a good H-bond network! You have probably already seen it, but there is a brief write-up about the Objective on the blog.

It's difficult to tell without seeing your solution, but it sounds like your network is below 75% satisfied so it will not receive any bonus. It does seem strange that it reports 3 interface bonds if you only see 2 bonds that span the interface. That could be a bug -- can you share your solution with scientists?

That is helpful feedback about reporting the raw numbers for the satisfaction calculation! I think we should be able to address that.

Bautho's picture
User offline. Last seen 1 week 6 days ago. Offline
Joined: 02/16/2012
Groups: Go Science
Next time :)

Thanks for the reply, Brian.
Unfortunately I did not have time anymore for the puzzle and will share my solutions with the next puzzles :)

User login
Download links:
  Windows    OSX    Linux  
Windows
(7/8/10)
OSX
(10.12 or later)
Linux
(64-bit)

Are you new to Foldit? Click here.

Are you a student? Click here.

Are you an educator? Click here.
Social Media


Search
Only search fold.it
Other Games: Mozak
Recommend Foldit
Topics
Top New Users
Sitemap

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