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


176eelko09 46 1295  11,4371
177Ben666 46 1295  11,4341
178FScot 46 1295  11,4171
179reefyrob 46 1295  11,4151
180crawlee34225 46 1295  11,4141
181spirogyra 46 1295  11,4071
182Hyacinth04 46 1295  11,3941
183chansuke 46 1295  11,3941
184AeneasIII 46 1295  11,3881
185screenshot 46 1295  11,3841
186pharoah 46 1295  11,3731
187Xanthie 46 1295  11,3651
188tela 46 1295  11,3571
189PTEver 46 1295  11,3461
190Xyphoid 46 1295  11,3321
191itskimo 46 1295 foldeRNA11,3311
192lacie 46 1295  11,3271
193bugmenot 46 1295  11,3221
194Schleicher 46 1295 SETI.Germany11,3221
195nmos1056 46 1295  11,3221
196AnjaM 46 1295  11,3211
197steamywindow 46 1295  11,3161
198Sadler 46 1295 Russian team11,3131
199Tock 46 1295  11,3111
200oxysmo 46 1295  11,2961

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beta_helix's picture
User offline. Last seen 53 min 2 sec 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 53 min 2 sec 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