1016: Unsolved VEGF protein: Server Starts

Closed since over 11 years ago

Summary

• Created: November 18, 2014
• Expires: December 01, 2014 at 14:00 UTC
• Max points: 100

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.

Top groups

• 1. Anthropic Dreams 100 pts. 9,183
• 2. Beta Folders 87 pts. 9,153
• 3. Void Crushers 75 pts. 9,145
• 4. Go Science 64 pts. 9,141
• 5. Contenders 55 pts. 9,110
• 6. Gargleblasters 47 pts. 9,063
• 7. Deleted group pts. 9,025
• 8. L'Alliance Francophone 33 pts. 9,009
• 9. FoldIt@Netherlands 28 pts. 8,929
• 10. Russian team 23 pts. 8,905

Top soloists

• 1. grogar7 100 pts. 9,169
• 2. retiredmichael 99 pts. 9,153
• 3. spmm 98 pts. 9,145
• 4. Bruno Kestemont 97 pts. 9,141
• 5. TheGUmmer 96 pts. 9,133
• 6. Madde 95 pts. 9,115
• 7. gmn 94 pts. 9,110
• 8. johnmitch 93 pts. 9,107
• 9. Vredeman 92 pts. 9,106
• 10. Timo van der Laan 91 pts. 9,097

Comments

[beta_helix]

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.
  ______

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

[jstoddard]

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]

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!