568: Beginner CASP10 Refinement Puzzle: TR644

Closed since almost 14 years ago

Summary

• Created: June 03, 2012
• Expires: June 10, 2012 at 19:00 UTC
• Max points: 100

Description

This is the first CASP10 Refinement Target. This model was the best server prediction for target T0644, generated by the SAM-T08 server. We've been told that ~85% of this model matches the native, so you just need to find which 15% to refine! More info in the puzzle comments.

Top groups

• 31. Eὕρηκα! Heureka! 1 pt. 10,860
• 32. SETIKAH@KOREA 1 pt. 10,834

Top soloists

• 301. LukasMinar 1 pt. 10,608
• 302. cmonman 1 pt. 10,598
• 303. skrystal94 1 pt. 10,592
• 304. baseballfreak43 1 pt. 10,585
• 305. heebus 1 pt. 10,554
• 306. kstater92 1 pt. 10,487
• 307. panthael 1 pt. 10,458
• 308. peacegabi 1 pt. 10,458
• 309. chopstikkx 1 pt. 10,414
• 310. Susume 1 pt. 10,414

Comments

[beta_helix]

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=90&view=refinement

This was the page for the previous Foldit puzzles for this protein:
http://fold.it/portal/node/992552#comment-17172
and:
http://fold.it/portal/node/992650#comment-17486

You'll notice that indeed that previous puzzle had a register shift (assuming this starting model is correct in that region).

Note that the organizers give us this as a hint:

"Starting model's GDT_TS=85. Residues 1-25 are absent from the experimental structure and deleted from the model."

So, unfortunately the first 25 residues have been deleted (and we'll never know where that helix went, it was probably a transmembrane anchor.) Therefore residue #1 on this puzzle corresponds to residue #26 on the previous versions.

GDT_TS=85 essentially means that 85% of the model superimposes correctly onto the native structure:

en.wikipedia.org

Global distance test

The global distance test (GDT), also written as GDT_TS to represent "total score", is a measure of similarity between two protein structures with known amino acid correspondences (e.g. identical amino acid sequences) but different tertiary structures. It is most commonly used to compare the results of protein structure prediction to the experimentally determined structure as measured by X-ray crystallography, protein NMR, or, increasingly, cryoelectron microscopy. The metric was developed by Ada...

[Susume]

Do we know which SAM-T08 model was the best?

[beta_helix]

We believe that SAM-T08-server_TS1.pdb is identical to the refinement model (except that it obviously doesn't have the first 25 residues trimmed!).