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991: 60 Residue Monomer Design: SS Design
Status: Closed

Summary

Name: 991: 60 Residue Monomer Design: SS Design
Status: Closed
Created: 09/30/2014
Points: 100
Expired: 10/08/2014 - 23:00
Difficulty: Intermediate
Description: In natural proteins, different amino acids show different propensities for forming secondary structures like alpha helices and beta strands. This puzzle includes a new Secondary Structure Design filter that restricts the use of GLY residues in helices and sheets. There are several other filters in effect; see the puzzle comments for details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!
Categories: Design, Overall

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Comments

bkoep's picture
User offline. Last seen 48 min 2 sec ago. Offline
Joined: 11/15/2012
Groups: None
Filters

Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence: Ensures that at least 25% of the residues are buried in the core of your design.

Fragment Score: Scans for parts of your design that are unlikely to fold up naturally. Use Rebuild and Remix tools to fix these regions of your design!

Secondary Structure: Checks that at least 25% of residues are in sheets; penalties are incurred if fewer than 25% of residues form sheets.

Secondary Structure Design: Penalizes GLY residues in helices and sheets.

Joined: 12/06/2008
Groups: Contenders
How does the Secondary Structure Design know?

How does the Secondary Structure Design know if a glycine is in a sheet or helix?

brow42's picture
User offline. Last seen 3 days 14 hours ago. Offline
Joined: 09/19/2011
Groups: None
It looks at bonding

The DSSP filter checks to see if a segment has (ideally) two hbonds to another distant segment (antiparallel sheet) or two adjacent segments (parallel sheets) or to the segment exactly 4 upstream (helix). It probably also has some smoothing, like making sure the bonding pattern continues for at least 2 or 3 segments in a row. I don't think the DSSP algorithm looks at angles at all, but it might do that to supplement the bonding information.

bkoep's picture
User offline. Last seen 48 min 2 sec ago. Offline
Joined: 11/15/2012
Groups: None
Yes

brow42 is correct. The Secondary Structure filter and the Secondary Structure Design filter both use the DSSP algorithm. DSSP defines helices and sheets based on hydrogen bonding patterns alone.*

(*I believe DSSP can use bond angles to discern certain types of loops, but this is not used in Foldit.)

Joined: 08/09/2010
add and delete segs

It would have been nice enable it. Without add/delete you have to start from zero if you want to change a bit your design

bkoep's picture
User offline. Last seen 48 min 2 sec ago. Offline
Joined: 11/15/2012
Groups: None
Thanks for the feedback

This was an oversight on our part. We'll make sure players can insert/delete segments next time!

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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, Microsoft, Adobe, RosettaCommons