puzzle picture
576: CASP10 Refinement Puzzle: TR661
Status: Closed


201GeoffreyY 46 1293  11,2961
202lb494 46 1293  11,2641
203Kevonni 46 1293  11,2631
204ten_string 46 1293  11,2581
205bull 46 1293 Team China11,2561
206ZeroLeak7 32 27 7Monkeys11,2501
207Uganalandia 46 1293 11,2491
208nLaptop 46 1293  11,2471
209bogy 46 1293  11,2431
210Tac1 46 1293  11,2421
211martinf 46 1293  11,2401
212nickbobbitt2015 46 1293  11,2251
213Alex333 46 571  11,2201
214Arne Heessels 46 336  11,2051
215coffee_coffee 46 1293  11,2021
216monkry 46 67  11,1791
217Aykroyd 46 1293  11,1761
218blob_folder 46 1293 7Monkeys11,1001
219treefish 46 1293  11,0981
220justjustin 46 1293 Anthropic Dreams11,0511
221blored 46 1293  11,0441
222Yuki 46 1293  11,0131
223DomDom88 46 1293  11,0011
224Le bleu 46 1293  10,9921
225Schnecke 46 1293  10,9501

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beta_helix's picture
User offline. Last seen 14 hours 38 min 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:

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 14 hours 38 min ago. Offline
Joined: 05/09/2008
Groups: None
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, Boehringer Ingelheim, RosettaCommons