beta_helix's picture
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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
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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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