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991: 60 Residue Monomer Design: SS Design

Closed since over 11 years ago

Intermediate Overall Design

Summary

Created
September 30, 2014
Expires
Max points
100
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!

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Comments

bkoep Staff Lv 1

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.

brow42 Lv 1

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.

BitSpawn Lv 1

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 Staff Lv 1

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

bkoep Staff Lv 1

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.)