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576: CASP10 Refinement Puzzle: TR661
Status: Closed

Groups

RankGroupScorePoints
1Go Science12,818100
2Anthropic Dreams12,80075
3Contenders12,71055
4Void Crushers12,68140
5putting the eat in meat12,68128
6foldeRNA12,66020
7L'Alliance Francophone12,64514
8FoldIt@Netherlands12,6069
9Team Hungary12,5276
10Another Hour Another Point12,4584
11Russian team12,3363
12Team China12,2662
13Gargleblasters12,2211
14Mojo Risin'12,1291
15SETI.Germany11,9451
16Freedom Folders11,7841
17Nerdfighters11,6151
18Czech National Team11,4731
19Biology-4th11,4631
207Monkeys11,2501
21BOINC.Italy11,2491
22Skeptics Guide to the Universe10,8771
23Geekdo10,2041
24DSN @ Home9,1101
25Team Germany7,5401


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beta_helix's picture
User offline. Last seen 8 hours 56 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=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 8 hours 56 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
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