Placeholder image of a protein
Icon representing a puzzle

583: Large CASP10 Refinement Puzzle: TR689

Closed since almost 14 years ago

Intermediate Overall Prediction

Summary

Created
June 24, 2012
Expires
Max points
100
Description

The seventh CASP10 Refinement Target has 234 residues! This model was the best server prediction for target T0689, generated by the Jiang_Fold server. We've been told that ~87% of this model matches the native, so you just need to find which 13% to refine! We are giving you a couple extra days to work on this one due to its size. More info in the puzzle comments.

Top groups

  1. Avatar for Deleted group 11. Deleted group pts. 13,990
  2. Avatar for Richard Dawkins Foundation 12. Richard Dawkins Foundation 10 pts. 13,950
  3. Avatar for Atlanta 13. Atlanta 7 pts. 13,883
  4. Avatar for Russian team 14. Russian team 6 pts. 13,866
  5. Avatar for SETI.Germany 15. SETI.Germany 4 pts. 13,728
  6. Avatar for Gargleblasters 16. Gargleblasters 3 pts. 13,702
  7. Avatar for 7Monkeys 17. 7Monkeys 2 pts. 13,660
  8. Avatar for Natural Abilities 18. Natural Abilities 2 pts. 13,515
  9. Avatar for Extraterrestrials 19. Extraterrestrials 1 pt. 13,506
  10. Avatar for Deleted group 20. Deleted group pts. 13,458
  1. Avatar for jogie62 111. jogie62 Lv 1 10 pts. 13,837
  2. Avatar for pgiles 112. pgiles Lv 1 9 pts. 13,826
  3. Avatar for reefyrob 113. reefyrob Lv 1 9 pts. 13,812
  4. Avatar for Deleted player 114. Deleted player pts. 13,800
  5. Avatar for Roukess 115. Roukess Lv 1 9 pts. 13,798
  6. Avatar for FreeFolder 116. FreeFolder Lv 1 8 pts. 13,796
  7. Avatar for jtollenaar 117. jtollenaar Lv 1 8 pts. 13,786
  8. Avatar for drjr 118. drjr Lv 1 8 pts. 13,785
  9. Avatar for Petrifolder 119. Petrifolder Lv 1 8 pts. 13,776
  10. Avatar for micheldeweerd 120. micheldeweerd Lv 1 7 pts. 13,772

Comments

beta_helix Staff Lv 1

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=132

Note that the organizers gave us this hint:

"Starting model GDT_TS=87."

GDT_TS=87 essentially means that 87% of the model superimposes correctly onto the native structure:

We believe that Jiang_Fold_TS1.pdb is identical to the refinement model.

Here is the sequence logo predicted by the SAM server:

H = helix
E = sheet
C = loop (or coil)

The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.

For example, the Valines at residues 34, 49, 54, 57, 66, 71 & 183 are highly predicted to be in sheets. However, the Valines at residues 3, 107, 137 & 144 are predicted to be anything.

spmm Lv 1

Just a note - on an ok machine (i7-720QM) with 8GB RAM, foldit and a browser running it is taking 6-7 minutes to run Blue Fuse.