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1016: Unsolved VEGF protein: Server Starts
Status: Closed

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beta_helix's picture
User offline. Last seen 6 hours 59 min ago. Offline
Joined: 05/09/2008
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Additional info:

Please read the recent blog entry about this unsolved protein.
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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.

Note that these secondary structure predictions are not necessarily present in the server model that has been provided in the puzzle.
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If you are a new Foldit player, please make sure you have completed all these tutorials before trying this puzzle:
- lonely sheets,
- lock and lower,
- rebuild,
- structure and rebuild,
- control over clashing.
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Solutions from Puzzle 1012 are not allowed to be loaded into this round, as we'd like you to focus on refining these server predictions.
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Here is the link to the Zhang Server website (where you can find a lot of detailed info such as templates used and predicted per-residue accuracy for each model):
http://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S200050

Joined: 10/28/2014
Groups: DCC Folders
best use of resources

Many dedicated players already run homology models across various servers before deciding on a fold to utilize. Were you trying to discover a new fold that is not precedented for this family of proteins? The puzzle 1016 makes more scientific sense to me compared to the puzzle 1012.

beta_helix's picture
User offline. Last seen 6 hours 59 min ago. Offline
Joined: 05/09/2008
Groups: None
Great question, jstoddard.

As we mentioned in 1012's puzzle description, homology-based methods have failed to solve this protein... this is why we wanted to give you an initial round without any bias from the various homologs.

It's a lot harder to ask you to do that once we've presented you with template-based server predictions!

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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