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568: Beginner CASP10 Refinement Puzzle: TR644
Status: Closed

Summary

Name: 568: Beginner CASP10 Refinement Puzzle: TR644
Status: Closed
Created: 06/03/2012
Points: 100
Expired: 06/10/2012 - 19:00
Difficulty: Beginner
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.
Categories: CASP10, Overall, Prediction

Top Groups

RankGroupScorePoints
1Anthropic Dreams11,748100
2Void Crushers11,71080
3Gargleblasters11,70963
4Go Science11,70850
5Team Hungary11,69639

Top Evolvers

Top Soloists

RankPlayerGroupScorePoints
1Galaxie 2 2  11,754100
2Close At&n... 78 1437  11,72398
3frood66 55 12 Gargleblasters11,70997
4Rav3n_pl 78 1437 Anthropic Dreams11,70995
5pauldunn 61 435 Go Science11,70793


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Comments

beta_helix's picture
User offline. Last seen 1 hour 13 min ago. Offline
Joined: 05/09/2008
Groups: None
More info here:

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:
http://en.wikipedia.org/wiki/Global_distance_test

Susume's picture
User offline. Last seen 8 hours 20 min ago. Offline
Joined: 10/02/2011
Do we know which SAM-T08

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

beta_helix's picture
User offline. Last seen 1 hour 13 min ago. Offline
Joined: 05/09/2008
Groups: None
Model 1:

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!).

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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