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2266: Electron Density Reconstruction 27

Closed since about 3 years ago

Novice Overall Prediction Electron Density

Summary

Created
February 07, 2023
Expires
Max points
100
Description

The structure of this protein has already been solved and published, but close inspection suggests that there are some problems with the published solution. We'd like to see if Foldit players can use the same electron density data to reconstruct a better model.

Sequence
MDETGKELVLVLYDYQEKSPREVTIKKGDILTLLNSTNKDWWKIEVNDRQGFVPAAYLKKLD

Top groups

  1. Avatar for VeFold 11. VeFold 1 pt. 16,106
  2. Avatar for AlphaFold 12. AlphaFold 1 pt. 16,106
  3. Avatar for BOINC@Poland 13. BOINC@Poland 1 pt. 15,965
  4. Avatar for Foldit Staff 14. Foldit Staff 1 pt. 14,385
  1. Avatar for Sandrix72
    1. Sandrix72 Lv 1
    100 pts. 16,327
  2. Avatar for LociOiling 2. LociOiling Lv 1 94 pts. 16,324
  3. Avatar for Galaxie 3. Galaxie Lv 1 88 pts. 16,321
  4. Avatar for MicElephant 4. MicElephant Lv 1 83 pts. 16,298
  5. Avatar for Timo van der Laan 5. Timo van der Laan Lv 1 78 pts. 16,294
  6. Avatar for gmn 6. gmn Lv 1 73 pts. 16,283
  7. Avatar for guineapig 7. guineapig Lv 1 68 pts. 16,280
  8. Avatar for Bletchley Park 8. Bletchley Park Lv 1 63 pts. 16,280
  9. Avatar for BootsMcGraw 9. BootsMcGraw Lv 1 59 pts. 16,280
  10. Avatar for NinjaGreg 10. NinjaGreg Lv 1 55 pts. 16,279

Comments

grogar7 Lv 1

Tell us more about the little dot that identifies as residue #1 Glycine, and is not attached to the rest of the protein?

LociOiling Lv 1

Weird, a solution loaded at 2,292 after being saved at 15,893. The 2292 killed a version of DRemix that's been working a long time. Not sure what's wrong with this one.

LociOiling Lv 1

Shared with scientists, a second one saved on 15,893, which loads at 2,298. The damaged load also manages to break some fancy Lua code related to getting the density score for a section. Regular old DRemix doesn't have that problem.

LociOiling Lv 1

See more comments in #bugs-and-feedback. The damaged solutions end up with around -3,000 ideality in 4 segments, totalling up to a roughly 13,000 point loss.

LociOiling Lv 1

See also https://fold.it/forum/bugs/saved-solutions-for-puzzle-2266-lose-score

The sequence is a another mystery here. The sequence shown on this page is an exact match for PDB 1E6H.

The puzzle starts with G for glycine in segement 1. The puzzle shows segment 1 as just a small sphere, not a normal-looking segment at all.

The puzzle ended up with gaps between 1-2 and 31-32. So the alignment ends up looking like this:

mdetgkelvlvlydyqeksprevtikkgdiltllnstnkdwwkievndrqgfvpaaylkkld (1E6H)
    g elvlvlydyqeksprevtikkgdiltllns nkdwwkievndrqgfvpaaylkkld (puzzle 2262)
    1 234567890123456789012345678901 2345678901234567890123456
              1         2         3          4         5

The two gaps in the sequence seem to be the source of the problem with saved solutions.