1667: "Too Much Density!" Freestyle puzzle

Closed since almost 7 years ago

Summary

• Created: April 25, 2019
• Expires: May 06, 2019 at 07:00 UTC
• Max points: 100

Description

This Electron Density puzzle is different than anything we've ever posted before! The extended chain is 187 residues long, but we are giving you a lot more density than that. You'll need to find where to fit this chain in the giant blob of density. (The "Trim Density" tool will be your friend)

Top groups

• 1. Go Science 100 pts. 22,258
• 2. Beta Folders 73 pts. 20,387
• 3. Anthropic Dreams 52 pts. 20,350
• 4. Gargleblasters 36 pts. 20,245
• 5. Russian team 24 pts. 20,076
• 6. Hold My Beer 16 pts. 20,019
• 7. Void Crushers 10 pts. 19,955
• 8. Marvin's bunch 6 pts. 19,897
• 9. HMT heritage 4 pts. 19,876
• 10. L'Alliance Francophone 2 pts. 19,761

Top soloists

• 1. fiendish_ghoul 100 pts. 22,033
• 2. Bautho 97 pts. 21,534
• 3. Bruno Kestemont 94 pts. 21,104
• 4. Galaxie 91 pts. 20,343
• 5. johnmitch 88 pts. 20,331
• 6. LociOiling 85 pts. 20,264
• 7. pvc78 82 pts. 20,240
• 8. Deleted player pts. 20,239
• 9. Susume 77 pts. 20,203
• 10. vakobo 74 pts. 20,076

Comments

[frood66]

thanks for those comments :)

[Susume]

I would love to be given this ED again with designable residues (let us pick all glycine for example) so we could design into the backbone only (or add just a few sidechains if we see a good spot). Would you consider offering us such a puzzle, and then trying out the subtraction method to see if it helps to make sidechains visible in the density? It could go in the experimental category.

[Bruno Kestemont]

If it has been an unsolved puzzle, I guess no player had found anything.

I tried during hours without being able to even find a starting position. Then I/we moved to a visual copy of the 5MRW, yet the result is poor.

I evolved the top solution and I'm ranked 3 for another solution + I shared to scientists 5 more high scoring solutions: it's obvious that none of them are even close to a realistic structure (the 5MRW solved one). Sidechains out of the cloud, one protein helix jumping through 2 "cloud helices" etc.

What would have helped us (in a case of unsolved protein)?

-some PSIPRED or other SS prediction
-partial solving of the other chains would have been on great help (in order to be able to erase other parts of the protein, or to be told to accept unburied helices - I would never have accepted this unburied helix starting seg 1 as a right solution without seeing it in the 5MRW)
-the erase tool (in my old&slow computer case, no erasing means no possibility to hand fold)
-contact map or any other help
-any tool or model that would help us to find the aromatics in the cloud (I like the GLY idea above)

[Bruno Kestemont]

That would be great if the player could do it 'on the fly':

-give me a PSIPRED prediction

-let me "mutate" everything to GLY

-using that I can move pieces of helices and sheets in the cloud in order to construct my sidechain highlights.

-then I use a new foldit tool to re-calculate the density cloud (with more weight to what I identified to be sidechains)

-then I "mutate" everything back to the protein sequence

-and I find-tune the cloud position

(otherwise, you ask us a first round with PSIPRED and sequence information, but all-GLY and an extra-weight for ED bonus, then you give us a second round with the real sequence in protein)

[bertro]

I wonder if some Side-by-side comparison of W and Y (and some other maybe) relative to resolution would be useful to us in visualizing cloud shape for said resolution?