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642: CASP ROLL Target R0022
Status: Closed

Summary

Name: 642: CASP ROLL Target R0022
Status: Closed
Created: 10/16/2012
Points: 100
Expired: 10/25/2012 - 18:00
Difficulty: Advanced
Description: Another CASP ROLL target. We are again providing you with 3 very different templates for now, and will give you with some server predictions once they are released. More details about this CASP target are in the puzzle comments.
Categories: CASP ROLL, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 19 hours 47 min ago. Offline
Joined: 05/09/2008
Groups: None
Additional info about this CASP Roll target

Here is the CASP link for this target (showing the amino acid sequence):
http://predictioncenter.org/casproll/target.cgi?id=65

You'll notice that the sequence we have given you has been trimmed (compared to the one on the CASP ROLL website). This is because the N-terminus is predicted to be a signal peptide by the Rosetta Server:
http://rosettaserver.bakerlab.org/results.jsp?id=34143

For more info on that: http://en.wikipedia.org/wiki/Signal_peptide
____________________________________________________

The SAM server had problems due to a power outage, but here is a close sequence logo (just missing the first 3 residues):

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 75, 89 & 92 are highly predicted to be part of a sheet. However, the Valine at residue 9 is not predicted to be anything!

The above predictions are already on the starting model (based on the horizontal lines in the above figure).
____________________________________________________

Link to template PDBs:

http://www.pdb.org/pdb/explore/explore.do?structureId=1qhq http://www.pdb.org/pdb/explore/explore.do?structureId=2qnk http://www.pdb.org/pdb/explore/explore.do?structureId=1avw

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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