Placeholder image of a protein
Icon representing a puzzle

828: Abeta Loop Closure A

Closed since about 12 years ago

Intermediate Overall Design

Summary

Created
December 24, 2013
Expires
Max points
100
Description

This puzzle builds on a piecewise design solution from Puzzle 808. Build loops to close the cutpoints between secondary structure elements to create an Abeta-binding protein! The two starting structures were derived from a single solution by Grom and Rita_Gat, but have different loop arrangements. Reset the puzzle to cycle through both starting structures. See the puzzle comments for more details. This puzzle will be open for two weeks.

Top groups

  1. Avatar for Contenders
    1. Contenders
    100 pts. 12,238
  2. Avatar for Beta Folders 2. Beta Folders 79 pts. 12,095
  3. Avatar for Void Crushers 3. Void Crushers 61 pts. 11,985
  4. Avatar for Brony@Home 4. Brony@Home 47 pts. 11,821
  5. Avatar for Anthropic Dreams 5. Anthropic Dreams 35 pts. 11,813
  6. Avatar for L'Alliance Francophone 6. L'Alliance Francophone 26 pts. 11,765
  7. Avatar for Gargleblasters 7. Gargleblasters 19 pts. 11,637
  8. Avatar for Fold for Science 1 8. Fold for Science 1 14 pts. 11,534
  9. Avatar for Russian team 9. Russian team 10 pts. 11,520
  10. Avatar for Deleted group 10. Deleted group pts. 11,306
  1. Avatar for spvincent
    1. spvincent Lv 1
    100 pts. 12,234
  2. Avatar for retiredmichael 2. retiredmichael Lv 1 98 pts. 12,091
  3. Avatar for dembones 3. dembones Lv 1 96 pts. 12,016
  4. Avatar for motu 4. motu Lv 1 94 pts. 12,015
  5. Avatar for Timo van der Laan 5. Timo van der Laan Lv 1 92 pts. 11,985
  6. Avatar for gitwut 6. gitwut Lv 1 90 pts. 11,948
  7. Avatar for spmm 7. spmm Lv 1 87 pts. 11,923
  8. Avatar for johnmitch 8. johnmitch Lv 1 85 pts. 11,846
  9. Avatar for Pagdzin 9. Pagdzin Lv 1 83 pts. 11,821
  10. Avatar for karstenw 10. karstenw Lv 1 81 pts. 11,783

Comments

bkoep Staff Lv 1

We've tried to estimate the number of residues required to close each loop, but you may prefer to distribute these residues differently. You can delete residues from one loop and reinsert them into another, although you cannot add additional residues to this puzzle.

There is no RMSD filter for this puzzle, but there are some constraints to help keep the secondary structure pieces in place. Note also that you can wiggle the backbone of the Abeta peptide, although there are constraints to keep the two Abeta strands in a sheet.

Bletchley Park Lv 1

You forgot to mention that this puzzle REQUIRES the latest client. Older clients will give an error message and refuse to load this puzzle.

Bletchley Park Lv 1

You forgot to mention that this puzzle REQUIRES the latest client. Older clients will give an error message and refuse to load this puzzle.

v_mulligan Lv 1

Ah, true – the puzzle does require the latest version of the game. We found a few bugs that appeared with puzzles that had cutpoints in the starting configuration, so the programmers had to fix those before we released this puzzle.

wisky Lv 1

Abeta backbone free?

Why is the abeta backbone free? All the other puzzles in this series have had the backbone of abeta locked.

bkoep Staff Lv 1

We know that the Abeta peptide is pretty flexible in solution, and is very likely to change shape upon binding—especially if the new shape makes better interactions with the binding protein. We do expect that these changes would be small, and that the peptide will generally favor a two-stranded beta sheet.