Placeholder image of a protein
Icon representing a puzzle

579: Beginner CASP10 Refinement Puzzle: TR662

Closed since over 13 years ago

Beginner Overall Prediction

Summary

Created
June 15, 2012
Expires
Max points
100
Description

This is the fourth CASP10 Refinement Target. This model was the best server prediction for target T0662, generated by the Zhang server. We've been told that ~84% of this model matches the native, so you just need to find which 16% to refine! More info in the puzzle comments.

Top groups

  1. Avatar for Go Science
    1. Go Science
    100 pts. 9,937
  2. Avatar for Contenders 2. Contenders 81 pts. 9,937
  3. Avatar for Anthropic Dreams 3. Anthropic Dreams 64 pts. 9,919
  4. Avatar for L'Alliance Francophone 4. L'Alliance Francophone 50 pts. 9,918
  5. Avatar for Void Crushers 5. Void Crushers 39 pts. 9,913
  6. Avatar for HMT heritage 6. HMT heritage 30 pts. 9,894
  7. Avatar for foldeRNA 7. foldeRNA 23 pts. 9,885
  8. Avatar for FoldIt@Netherlands 8. FoldIt@Netherlands 17 pts. 9,821
  9. Avatar for Deleted group 9. Deleted group pts. 9,819
  10. Avatar for Russian team 10. Russian team 9 pts. 9,784
  1. Avatar for MalcolmW 241. MalcolmW Lv 1 1 pt. 9,331
  2. Avatar for Bewable 242. Bewable Lv 1 1 pt. 9,157
  3. Avatar for jflat06 243. jflat06 Lv 1 1 pt. 8,368
  4. Avatar for histon 244. histon Lv 1 1 pt. 8,368
  5. Avatar for dbuske 245. dbuske Lv 1 1 pt. 8,368
  6. Avatar for ingoneato 246. ingoneato Lv 1 1 pt. 8,368
  7. Avatar for calvino80 247. calvino80 Lv 1 1 pt. 8,368
  8. Avatar for mxynidis 248. mxynidis Lv 1 1 pt. 8,368
  9. Avatar for MCXCI 249. MCXCI Lv 1 1 pt. 8,368
  10. Avatar for gdnskye 250. gdnskye Lv 1 1 pt. 8,368

Comments

beta_helix Staff Lv 1

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=110&view=refinement

Note that the organizers give us this as a hint:

"N-term res. 1-4 are disordered in the native structure and removed from the starting model. Starting GDT_TS=84."

So, the first 4 residues have been deleted.

GDT_TS=84 essentially means that 84% of the model superimposes correctly onto the native structure:

We believe that Zhang-Server_TS4.pdb is identical to the refinement model (except that it obviously doesn't have the first 4 residues trimmed!)

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 8, 11, 35-36, 62 & 69 are highly predicted to be part of a helix. However, the Valines at residues 49 & 52 are predicted to be in either loops or sheets.