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


126jobo0502 46 22 L'Alliance Francophone11,8481
127SouperGenious 46 1399  11,8431
128rinze 46 38  11,8381
129nemo7731 46 1399  11,8361
130duran2101 46 1399 Go Science11,8091
131weurhartdezirez 46 1399 Freedom Folders11,7841
132m.a.g.e 46 1399  11,7791
133kdieber 46 1399  11,7751
134JameAlec 46 1399  11,7731
135jezsissek 46 1399  11,7271
136mitarcher 46 1399  11,7221
137caglar 46 1399  11,7201
138bamh 46 52  11,7161
139ourtown 46 1399  11,7051
140hada 46 473  11,7021
141AIDA64 46 1399  11,6841
142heyubob 46 402  11,6731
143Brewster 46 1399 Anthropic Dreams11,6561
144Jesse Pinkman 46 1399  11,6461
145hkilik 46 1399  11,6411
146mirjamvandelft 46 1399  11,6241
147jdretired 46 1399  11,6241
148TheMan2000 46 1399 Nerdfighters11,6151
149GracielaW 46 1399  11,6111
150Steven Pletsch 46 396 11,6101

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beta_helix's picture
User offline. Last seen 3 hours 46 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 3 hours 46 min 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, Boehringer Ingelheim, RosettaCommons