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1773: Symmetric Trimer Design: H-Bond Networks
Status: Closed

Summary

Name: 1773: Symmetric Trimer Design: H-Bond Networks
Status: Closed
Created: 12/13/2019
Points: 100
Expired: 12/20/2019 - 23:00
Difficulty: Intermediate
Description: H-bond Networks are back! The H-bond Network Objective encourages players to bury 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! In this puzzle, there are no limits on the Complex Core, but we've included the Complex Core objective so players can see which residues count as core in the H-bond Networks.
Categories: Design, Overall, Symmetry

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1Gargleblasters22,885100
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Comments

bkoep's picture
User offline. Last seen 6 hours 9 min ago. Offline
Joined: 11/15/2012
Groups: None
Objectives

Core Existence: Monomer (max +2800)
Ensures that at least 28 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:
Rewards networks that comprise at least two 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.

spvincent's picture
User offline. Last seen 14 hours 19 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
Unsatisfied polars

I believe this point has cropped up before, but it would be nice if there was some way of determining what polar bonds are unsatisfied in an H-bond network.

bkoep's picture
User offline. Last seen 6 hours 9 min ago. Offline
Joined: 11/15/2012
Groups: None
You're right!

This is the most important aspect of H-bond networks! We're working on better detection of unsatisfied polar atoms already; we'll make sure that these atoms are clearly indicated, as well.

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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, RosettaCommons