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643: CASP ROLL Target R0021
Status: Closed


Name: 643: CASP ROLL Target R0021
Status: Closed
Created: 10/15/2012
Points: 100
Expired: 10/26/2012 - 06:00
Difficulty: Intermediate
Description: Here is the next CASP ROLL target. We are again providing you with 3 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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beta_helix's picture
User offline. Last seen 6 hours 27 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):

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:

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 1, 42 & 83 are highly predicted to be part of a sheet. However, the Valines at residues 9, 10 & 100 are 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=3dxe http://www.pdb.org/pdb/explore/explore.do?structureId=2jgb http://www.pdb.org/pdb/explore/explore.do?structureId=3na2

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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, Boehringer Ingelheim, RosettaCommons