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1007: 90 Residue Monomer Design: SS Design
Status: Closed

Summary

Name: 1007: 90 Residue Monomer Design: SS Design
Status: Closed
Created: 11/03/2014
Points: 100
Expired: 11/10/2014 - 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 SS 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 11 hours 5 min 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 30% 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 no more than 50% of residues are in helices; penalties are incurred if greater than 50% of residues form helices.

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

Joined: 10/30/2012
Groups: Beta Folders
might be time to drop this

might be time to drop this style of puzzle, even with a fast machine the filters make it balky.

spmm's picture
User offline. Last seen 17 weeks 6 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
Possibly let people separate the filters

In early stages of the game the fragment filter is doing a lot of work for no value, we usually know that loops in particular are less than optimal early on when we are trying to get the overal pose in place but have to turn all filters off, not just the fragment one. Just a thought.

Joined: 09/24/2012
Groups: Go Science
does the remix tool work ?

see
http://fold.it/portal/node/1998506

Does anybody have an example of a LUA remix command that did anything?

I abandoned using this tool even manually because I find it heavy to use (freeze or cut, remix with no change, unfreeze uncut). And my recipe does not work either.

bkoep's picture
User offline. Last seen 11 hours 5 min ago. Offline
Joined: 11/15/2012
Groups: None
Not always

The remix tool is not guaranteed to find a solution. Sometimes, there is no good fragment with the same endpoints as your selection, and you will need to alter your selection.

Are you finding that the Remix tool fails to find a solution every time you use it, without exception? Would you mind sharing such a solution with us, using the Share with Scientist option?

Blog post about Remix:
https://fold.it/portal/node/996301

spmm's picture
User offline. Last seen 17 weeks 6 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
time taken

On a reasonably high spec end point on the 90 residue design puzzle - time taken for 1( that is one ) standard run of Blue Fuse on auto:

4.35 minutes with filters on
56 seconds with filters off

remix, couldn't find the nose on its face with both hands
and rebuild is just being silly even on small sections

spmm's picture
User offline. Last seen 17 weeks 6 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
example puzzle

the example remix puzzle you have linked to is not a design puzzle

Joined: 06/06/2013
Groups: Gargleblasters
too difficult to work

posted this on wrong puzzle earlier. It took about 2 hours for my computer to run regular worm on this puzzle, maybe 3. I left it run 10-11 hours to get through walking rebuild at lengths 1 & 2 only. Many players have less power than I do. This is not workable for me
I do take responsibility for my bad decisions. but this still runs too slow for us ordinary humans. I won't do one like this again except by mistake

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