Placeholder image of a protein
Icon representing a puzzle

1885: Symmetric Trimer Design: H-bond Networks

Closed since over 5 years ago

Intermediate Overall Design Symmetry

Summary

Created
September 02, 2020
Expires
Max points
100
Description

Design a symmetric protein trimer, with 3 identical chains that assemble together! 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 made a subtle change to the scoring of H-bonds that should help to improve H-bond geometry for SER, THR, and TYR sidechains. 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.

Top groups

  1. Avatar for BOINC@Poland 11. BOINC@Poland 1 pt. 14,490
  2. Avatar for SETI.Germany 12. SETI.Germany 1 pt. 14,378
  3. Avatar for FoldIt@Netherlands 13. FoldIt@Netherlands 1 pt. 13,197
  4. Avatar for Italiani Al Lavoro 14. Italiani Al Lavoro 1 pt. 10,761
  5. Avatar for Trinity Biology 15. Trinity Biology 1 pt. 10,662
  6. Avatar for Team Canada 16. Team Canada 1 pt. 10,549
  7. Avatar for Foldit Staff 17. Foldit Staff 1 pt. 0
  1. Avatar for mirp
    1. mirp Lv 1
    100 pts. 18,651
  2. Avatar for silent gene 2. silent gene Lv 1 85 pts. 18,645
  3. Avatar for ichwilldiesennamen 3. ichwilldiesennamen Lv 1 71 pts. 18,617
  4. Avatar for Dhalion 4. Dhalion Lv 1 60 pts. 18,607
  5. Avatar for Czim 5. Czim Lv 1 49 pts. 18,607
  6. Avatar for Formula350 6. Formula350 Lv 1 41 pts. 18,547
  7. Avatar for Skippysk8s 7. Skippysk8s Lv 1 33 pts. 18,547
  8. Avatar for Mike Lewis 8. Mike Lewis Lv 1 27 pts. 18,543
  9. Avatar for HuubR 9. HuubR Lv 1 22 pts. 18,543
  10. Avatar for Keresto 10. Keresto Lv 1 17 pts. 18,533

Comments

bkoep Staff Lv 1

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).

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.