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641: CASP ROLL Target R0020
Status: Closed

Summary

Name: 641: CASP ROLL Target R0020
Status: Closed
Created: 10/11/2012
Points: 100
Expired: 10/21/2012 - 14:00
Difficulty: Intermediate
Description: CASP ROLL is back! We are providing you with 3 templates for now (in hope that one of them is correct), 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 2 days 16 hours 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=63

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=34040

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

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 16, 54 & 110 are highly predicted to be part of a sheet. However, the Valine at residue 89 is predicted to be in a loop!

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=3iuu
http://www.pdb.org/pdb/explore/explore.do?structureId=2jvf
http://www.pdb.org/pdb/explore/explore.do?structureId=1qys

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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, Microsoft, Adobe, RosettaCommons