puzzle picture
561: CASP10 Target T0678
Status: Closed

Summary

Name: 561: CASP10 Target T0678
Status: Closed
Created: 05/22/2012
Points: 100
Expired: 05/31/2012 - 18:00
Difficulty: Advanced
Description: Yet another tough one! None of the alignment programs were able to find good templates for this target, and it might be the case that this protein has no homologs. We are giving you 7 templates (in hope that one of them is correct) for now, and will provide you with some server predictions once they are released. More details about this CASP target are in the puzzle comments.
Categories: CASP10, Overall, Prediction

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1Contenders11,646100
2Anthropic Dreams11,56976
3Void Crushers11,52256
4foldeRNA11,42641
5Go Science11,40230

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Comments

beta_helix's picture
User offline. Last seen 13 hours 45 min ago. Offline
Joined: 05/09/2008
Groups: None
Additional info about this CASP target

Here is the CASP link for this target (showing the amino acid sequence):
http://predictioncenter.org/casp10/target.cgi?id=75
____________________________________________________

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 Valines at residues 40 & 85 are highly predicted to be in a helix. However, the Valine at residues 159 is predicted to be anything.
____________________________________________________

Link to template PDBs:

http://www.pdb.org/pdb/explore/explore.do?structureId=3jui
http://www.pdb.org/pdb/explore/explore.do?structureId=1paq
http://www.pdb.org/pdb/explore/explore.do?structureId=2hps
http://www.pdb.org/pdb/explore/explore.do?structureId=3ebb
http://www.pdb.org/pdb/explore/explore.do?structureId=1ls4
http://www.pdb.org/pdb/explore/explore.do?structureId=3rkv
http://www.pdb.org/pdb/explore/explore.do?structureId=3axy

Keep in mind that it's very likely that ONLY ONE of these templates is close to the native (if we're lucky!)

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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