1007: 90 Residue Monomer Design: SS Design

Closed since over 11 years ago

Summary

• Created: November 03, 2014
• Expires: November 10, 2014 at 23:00 UTC
• 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 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!

Top groups

• 1. Beta Folders 100 pts. 10,554
• 2. Anthropic Dreams 84 pts. 10,546
• 3. Contenders 70 pts. 10,510
• 4. Go Science 57 pts. 10,453
• 5. Gargleblasters 47 pts. 10,385
• 6. FoldIt@Netherlands 38 pts. 10,281
• 7. L'Alliance Francophone 30 pts. 10,257
• 8. Void Crushers 24 pts. 10,125
• 9. SETI.Germany 19 pts. 10,114
• 10. Deleted group pts. 9,982

Top soloists

• 1. BitSpawn 100 pts. 10,546
• 2. retiredmichael 98 pts. 10,525
• 3. MurloW 96 pts. 10,496
• 4. spvincent 94 pts. 10,440
• 5. karstenw 93 pts. 10,418
• 6. Googol30 91 pts. 10,383
• 7. pauldunn 89 pts. 10,383
• 8. grogar7 87 pts. 10,360
• 9. nemo7731 85 pts. 10,356
• 10. Hiro Protagonist 83 pts. 10,281

Comments

[bkoep]

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.

[retiredmichael]

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

[spmm]

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.

[Bruno Kestemont]

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]

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]

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
<end

[spmm]

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

[Skippysk8s]

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