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577: CASP10 Refinement Puzzle: TR688
Status: Closed

Summary

Name: 577: CASP10 Refinement Puzzle: TR688
Status: Closed
Created: 06/15/2012
Points: 100
Expired: 06/23/2012 - 01:00
Difficulty: Intermediate
Description: This target was originally 196 residues, but has been trimmed down to 185. We have been told that almost 78% of this model matches the native, so we are giving you the 3 templates that were used to generate this model. Maybe by moving the alignment around using the Alignment Tool you'll be able to completely match the native. More info in the puzzle comments.
Categories: CASP10, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 9 hours 52 min ago. Offline
Joined: 05/09/2008
Groups: None
Additional info about this CASP10 Refinement target

Here is the CASP link for this Refinement target:
http://predictioncenter.org/casp10/target.cgi?id=116&view=refinement
____________________________________________________

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 Leucines at residues 87 & 110-11 are highly predicted to be in a sheet. However, the Leucine at residue 20 is predicted to be anything.
____________________________________________________________

Note that we are giving you over 7 days to work on this one.
It's a large protein you have 3 templates to work with, so we hope that you will try changing the alignments on each of them.

beta_helix's picture
User offline. Last seen 9 hours 52 min ago. Offline
Joined: 05/09/2008
Groups: None
Enjoy beta_helix's favorite topology!

I hope you enjoy the structure of this protein.

I just wanted to add that like Puzzle 576, the starting model is not the one CASP gave us (which was another RosettaServer model). We have given you the closest non-Rosetta server model (it's only 1.12 Angstroms RMSD away from the model chosen by the CASP organizers) so that you will be able to find high-scoring solutions that are slightly different than the ~78% correct starting structure.

You can read more about the motivation for this here:
http://fold.it/portal/node/992952#comment-18289

Joined: 08/30/2011
favourite topology

indeed very very very cool!

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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