puzzle picture
886: CASP11 Target T0759: Server Models
Status: Closed

Summary

Name: 886: CASP11 Target T0759: Server Models
Status: Closed
Created: 05/02/2014
Points: 100
Expired: 05/10/2014 - 20:00
Difficulty: Intermediate
Description: This is the first CASP11 Foldit puzzle! This puzzle has 101 residues, and we've provided you with 5 Robetta server models (all generated from the same homology template). Restart the puzzle to cycle through the alternate starting structures.
Categories: CASP11, Overall, Prediction

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Comments

wisky's picture
User offline. Last seen 8 weeks 2 days ago. Offline
Joined: 07/13/2011
Number of residues

In the puzzle description, you say this target has 109 residues.

In game, it has 101.

One of these is a mistake, and I hope it's the description...

wisky's picture
User offline. Last seen 8 weeks 2 days ago. Offline
Joined: 07/13/2011
Possible Histidine tag removal?

Could be a possible histidine tag removal? No clue.

beta_helix's picture
User offline. Last seen 6 days 20 hours ago. Offline
Joined: 05/09/2008
Groups: None
Indeed it's the his tag

You can see that the RosettaServer ignored the first 8 residues:
http://rosettaserver.bakerlab.org/results.jsp?id=48098&p=1

I'll update the description, thanks for the catch!

wisky's picture
User offline. Last seen 8 weeks 2 days ago. Offline
Joined: 07/13/2011
Thanks!

Thanks, beta_helix. Scared me for a bit there ;)

Joined: 05/26/2008
Groups: Hold My Beer
Is there a SAM prediction for

Is there a SAM prediction for his puzzle ?

beta_helix's picture
User offline. Last seen 6 days 20 hours ago. Offline
Joined: 05/09/2008
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@Steven Pletsch

There is a SAM prediction, but that is for the full length of the target (including the his tag) so the numbering is all off.

It's probably easier to use the RosettaServer's secondary structure prediction (from PSIPRED): http://rosettaserver.bakerlab.org/results.jsp?id=48098&p=1

but here is the SAM sequence logo in case you are interested:
http://compbio.soe.ucsc.edu/SAM_T08/results/target08-query-1398960605-17570/T0759.dssp-ehl2-logo.pdf

Joined: 05/26/2008
Groups: Hold My Beer
Thank you both are helpful :)

Thank you both are helpful :)

jeff101's picture
User offline. Last seen 6 days 19 hours ago. Offline
Joined: 04/20/2012
Groups: Go Science
Please list starting scores for each model:

It would be helpful if you would list the starting scores for each of the 5 models shown at: http://rosettaserver.bakerlab.org/results.jsp?id=48098&p=1
Perhaps for future puzzles, you could list the score for each model under its image on pages like this. You could also do like structure.SetNote(1,'Model X 5238.408') to set a note for amino acid #1 in each structure saying which model it represents.

So far I have seen the following starting scores for puzzle 886:
5238.408
7097.759
7232.753
Can you list the remaining scores and to which model each of the 5 scores corresponds?

Thanks!

spmm's picture
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Joined: 08/05/2010
Groups: Void Crushers
Tab to see which structure it is

The structure number is listed in the tab popup, but not the start score. Only five models without alignments is a bit luxurious :)

jeff101's picture
User offline. Last seen 6 days 19 hours ago. Offline
Joined: 04/20/2012
Groups: Go Science
Model/Structure Numbers for Puzzle 886

Thanks, spmm. Now I see the model/structure numbers when I tab on amino acids. I also noticed that on my slower machines when I press "Reset Puzzle", the new model number appears like a level up/down message and then quickly disappears.

So here are the 5 models for 886 with their starting scores:
1 7097.759
2 6755.029
3 5238.408
4 7232.753
5 7116.894

jeff101's picture
User offline. Last seen 6 days 19 hours ago. Offline
Joined: 04/20/2012
Groups: Go Science
Robetta images of the models

Can we rotate the images for each model shown at http://rosettaserver.bakerlab.org/results.jsp?id=48098&p=1 ?
When I click on these images, a new screen appears that has 4 arrows and a larger version of the image, but so far I haven't found a way to make the image change/rotate. It also won't let me download the pdb files without a username and password, and these seem different from my Foldit username and password.

beta_helix's picture
User offline. Last seen 6 days 20 hours ago. Offline
Joined: 05/09/2008
Groups: None
You can download server models directly from the CASP website

The CASP organizers post the "stage2" server models 8 days after a target is released:
http://predictioncenter.org/download_area/CASP11/server_predictions/

So you can download T0759.stage2.3D.srv.tar.gz to get the PDB files for the BAKER-ROSETTASERVER predictions.

Here is more info about the stage1 vs stage2 datasets:
http://predictioncenter.org/news.cgi#178

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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