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576: CASP10 Refinement Puzzle: TR661
Status: Closed

Summary

Name: 576: CASP10 Refinement Puzzle: TR661
Status: Closed
Created: 06/13/2012
Points: 100
Expired: 06/22/2012 - 15:00
Difficulty: Intermediate
Description: This target was originally 215 residues, but has been trimmed down to 185. We have been told that almost 80% of this model matches the native, so we are also giving you the template that was used to generate this model. Hopefully by moving the alignment around with the Alignment Tool you'll be able to completely match the native! Please read the puzzle comments for more on this.
Categories: CASP10, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 1 day 1 hour ago. Offline
Joined: 05/09/2008
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Additional info about this CASP10 Refinement target

Here is the CASP link for this Refinement target:
http://predictioncenter.org/casp10/target.cgi?id=104&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 18-19, 22, 40 & 82 are highly predicted to be in a helix. However, the Leucine at residue 131 is predicted to be in a sheet.
____________________________________________________________

Note that we are giving you over 8 days to work on this one, because it's a large protein and TR688 will have to be due on the same day (they gave us less than 3 weeks to work on that one).

beta_helix's picture
User offline. Last seen 1 day 1 hour ago. Offline
Joined: 05/09/2008
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The starting model is not the one CASP gave us.

The model that the CASP organizers have given us for this Refinement Target is actually a RosettaServer model (generated using Rosetta@home).

The trouble with this (as we learned in CASP9, which you can read about here: http://depts.washington.edu/bakerpg/drupal/node/435) is that this model is already minimized with Rosetta so it will be very hard to move that model out of its local energy minimum.

So for the starting model, we have given you the closest non-Rosetta server model (that is only 1.2 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 ~80% correct starting structure.

In addition, we are providing you with the exact template and alignment that Rosetta used to generate that model, so you should be able to end up with the same structure as Rosetta (but without having it being heavily minimized). We also hope that by moving the alignment around you are able to increase the model accuracy from 80% to 100%.

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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