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556: CASP10 Target T0660
Status: Closed

Summary

Name: 556: CASP10 Target T0660
Status: Closed
Created: 05/10/2012
Points: 100
Expired: 05/19/2012 - 19:00
Difficulty: Advanced
Description: Here is the second CASP10 target. This target is 108 residues and we are giving you the top-predicted templates from 3 different alignment programs. Make sure to try out all 3 templates since we don't know which one is closer to the correct native structure! More details about this CASP target are in the puzzle comments.
Categories: CASP10, Overall, Prediction

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4Go Science10,69452
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Comments

beta_helix's picture
User offline. Last seen 11 hours 18 min ago. Offline
Joined: 05/09/2008
Groups: None
Additional info about this CASP target

Here is the CASP link for this target (which has the amino acid sequence):
http://predictioncenter.org/casp10/target.cgi?id=57

____________________________________________________

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 Valine at residue 74 is predicted to be part of a helix. However, the Valine at residue 26 is highly predicted to be in a sheet.

marie_s's picture
User offline. Last seen 1 year 20 weeks ago. Offline
Joined: 05/18/2008
Groups: None
templates pdb

Are these templates in pdb?
I will like to have the number, just to have a look on them.

Susume's picture
User offline. Last seen 1 day 8 hours ago. Offline
Joined: 10/02/2011
I found the templates in the

I found the templates in the Protein Data Bank (pdb.org) by searching for the name of each template: 4d8k, 1Lck, and 2kym. The picture they give for 1Lck is not great; it fails to show how similar it is to 4d8k. Here are some images of the three templates from pyMOL that may help.

1Lck yellow 4d8k blue1Lck yellow 4d8k blue
2kym2kym

beta_helix's picture
User offline. Last seen 11 hours 18 min ago. Offline
Joined: 05/09/2008
Groups: None
Thanks for posting that Susume

marie_s, any template that we will give you will be coming from the PDB. I will try to post a link to them in the puzzle comments.

Here are the ones from this puzzle (the same as Susume's screenshots):
http://www.pdb.org/pdb/explore/explore.do?structureId=4d8k
http://www.pdb.org/pdb/explore/explore.do?structureId=1lck
http://www.pdb.org/pdb/explore/explore.do?structureId=2kym

and as Susume mentioned you can always grab the pdb ID for any template by toggling the Name/Score button (in the far right column of the Alignment Tool) and typing that ID into www.pdb.org

krulon's picture
User offline. Last seen 5 years 33 weeks ago. Offline
Joined: 11/20/2010
Groups: foldeRNA
Shared template models?

My thanks also to Susume. I find the pictures of the alignment folds very interesting.

Sometimes when we have been given 10 alignment prediction templates, I have been threading all 10 and saving them individually. That allows me to load them, or load them as guides. I can then use the "align guide" tool to align certain portions of the folds. Sometimes, I find shared solutions/guides easier to visualize than the ball and chain representation we get with the "show alignment" tool.

If 200 people were to make and save 10 local solutions, it would seem like a tremendous waste of time. Could each of the alignment templates be some type of global "Shared Solution" or "Shared Template" available for everyone?

In this puzzle, it would have been nice to be able to open a "Shared Solution" model for each of the 3 proteins that were given to us as templates.

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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