puzzle picture
542: Advanced Alignment Cutpoint Puzzle
Status: Closed

Summary

Name: 542: Advanced Alignment Cutpoint Puzzle
Status: Closed
Created: 04/11/2012
Points: 100
Expired: 04/19/2012 - 23:00
Difficulty: Advanced
Description: This advanced puzzle requires using the new cutpoints in the Alignment Tool. There is only one template you can thread with, but unfortunately the alignment is incorrect. This is not a blind target, but is perfect practice for the Template-Based category in CASP 10. More info about this in the puzzle comments. Make sure to complete and understand Intro Puzzles 6-1 through 6-3 before attempting this difficult puzzle.
Categories: Overall, Prediction

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1Anthropic Dreams10,483100
2Void Crushers10,44581
3Contenders10,43064
4Go Science10,36251
5foldeRNA10,22340

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Comments

beta_helix's picture
User offline. Last seen 3 days 2 hours ago. Offline
Joined: 05/09/2008
Groups: None
Good practice for CASP 10

This puzzle is actually a CASP 9 target (T0552), which some of you might recognize from previous Foldit puzzles. (The results from previous puzzles finally led us to implementing the new cutpoints).

The native has been released, but it was solved using NMR and the ensemble of models has a lot of variation (as you can see below, this is WITH the termini trimmed):

NMR ensemble of 2L3B: First 10 models in NMR ensemble for 2L3BNMR ensemble of 2L3B: First 10 models in NMR ensemble for 2L3B

You can obviously examine the native all you want (and for fairness we are posting it here in the puzzle comments: http://www.rcsb.org/pdb/explore/explore.do?structureId=2l3b) but the goal of this puzzle is to help us all prepare for CASP 10, which starts in early May!

Clearly for CASP, there will be no natives, so we want to find out now if the current Alignment Tool is sufficient to perform well on the Template-Based targets.

WE KNOW THAT YOU WANT A SCISSOR TOOL TO PUT IN YOUR OWN CUTPOINTS :-) That will be added soon, but we want to make sure that the current cutpoint system does not have any major bugs.

Although you can just thread the starting alignment and massage/fold the protein to a decent conformation, we believe that initially moving the alignment around can result in a better starting model (making it easier to get close to the native). Obviously, this is what we want to find out... so please let us know!

Thank you and happy threading!

spmm's picture
User offline. Last seen 40 weeks 6 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
puzzle 369

would seem to be the earlier puzzle referred to in the text above. High scores there were 11062.xxx

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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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