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559: CASP10 Target T0673
Status: Closed

Summary

Name: 559: CASP10 Target T0673
Status: Closed
Created: 05/17/2012
Points: 100
Expired: 05/26/2012 - 21:00
Difficulty: Advanced
Description: This is 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. Again we are giving you 6 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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Comments

beta_helix's picture
User offline. Last seen 1 hour 17 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=70
____________________________________________________

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 6, 7, & 10 are highly predicted to be in a helix. However, the Valines at residues 59, 60, 64 & 65 are predicted to be in a sheet.
____________________________________________________

Link to template PDBs:

http://www.pdb.org/pdb/explore/explore.do?structureId=3s4k
http://www.pdb.org/pdb/explore/explore.do?structureId=1olp
http://www.pdb.org/pdb/explore/explore.do?structureId=2w9q
http://www.pdb.org/pdb/explore/explore.do?structureId=2e12
http://www.pdb.org/pdb/explore/explore.do?structureId=3e1e
http://www.pdb.org/pdb/explore/explore.do?structureId=1q6w

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