puzzle picture
608: Symmetric CASP10 Refinement Puzzle: TR722
Status: Closed

Summary

Name: 608: Symmetric CASP10 Refinement Puzzle: TR722
Status: Closed
Created: 07/28/2012
Points: 100
Expired: 08/06/2012 - 23:59
Difficulty: Intermediate
Description: This is the eighteenth CASP10 Refinement Target. This model was the best server prediction for target T0722, generated by the BAKER-ROSETTASERVER (using Rosetta@home). Despite being the prediction closest to the native, almost half of the model is incorrect: only ~58% of this model matches the solved structure. We believe that one possible reason is that this protein folds up as a dimer, so we are giving you the model with symmetry. Please read the puzzle comments for additional details.
Categories: CASP10, Overall, Prediction, Symmetry

Top Groups

RankGroupScorePoints
1Void Crushers15,108100
2Contenders14,95880
3Beta Folders14,95762
4foldeRNA14,88948
5Gargleblasters14,84837

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Comments

beta_helix's picture
User offline. Last seen 19 hours 4 min ago. Offline
Joined: 05/09/2008
Groups: None
More info here:

NOTE: The Cut Tool IS available for this symmetry puzzle, but only in the Developer Preview.
(If you want to try it out, please read "How do I try out the Foldit Developer Preview?" in the FAQ: http://fold.it/portal/info/faq )
Once the next update posts (early next week) the Cut Tool will be available in main.
__________________________________________________

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=195

Note that the organizers gave us this hint:

"Starting model GDT_TS=58."

GDT_TS=58 essentially means that ONLY 58% of the model superimposes correctly onto the native structure:
http://en.wikipedia.org/wiki/Global_distance_test

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 23, 55, 85, 94, 112 & 115 are highly predicted to be part of a helix. However, the Valine at residue 34 is not predicted to be anything.

beta_helix's picture
User offline. Last seen 19 hours 4 min ago. Offline
Joined: 05/09/2008
Groups: None
Possible Topologies

These were some of the possible templates for T0722:


This doesn't mean that TR722 folds up as a coiled-coil, but it might be a topology worth exploring.

We will try to post another Foldit Puzzle for TR722 where we give you just the starting model as a monomer (in case that it how the native folds up). It will likely be a very short puzzle.

beta_helix's picture
User offline. Last seen 19 hours 4 min ago. Offline
Joined: 05/09/2008
Groups: None
Images gone!

As pointed out here (http://fold.it/portal/node/993286) the above images have disappeared!

They can be found here:
http://fold.it/portal/files/images/seqLogo_48.png
& below (just copy the entire link and paste it in your browser):
http://fold.it/portal/files/images/Screen shot 2012-07-28 at 2.03.54 PM.png
http://fold.it/portal/files/images/Screen shot 2012-07-28 at 2.04.17 PM.png
http://fold.it/portal/files/images/Screen shot 2012-07-28 at 2.04.55 PM_0.png

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons