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1016: Unsolved VEGF protein: Server Starts
Status: Closed

Summary

Name: 1016: Unsolved VEGF protein: Server Starts
Status: Closed
Created: 11/18/2014
Points: 100
Expired: 12/01/2014 - 14:00
Difficulty: Intermediate
Description: We are again giving you this unsolved vascular endothelial growth factor protein, but this time with 5 Zhang Server predictions as starting points. Resetting the puzzle will cycle through each model. We are giving you 2 weeks to work on this puzzle, so please try out each server start. Although one server model scores better than the rest initially, it might be the furthest from the native and might not get you the most points in the end! SAM secondary structure predictions are in the puzzle comments.
Categories: Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 15 hours 14 min ago. Offline
Joined: 05/09/2008
Groups: None
Additional info:

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

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.
________________

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.
________________

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.
________________

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 15 hours 14 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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