puzzle picture
901: CASP11 T0779: WeFold Round
Status: Closed

Summary

Name: 901: CASP11 T0779: WeFold Round
Status: Closed
Created: 05/25/2014
Points: 100
Expired: 06/01/2014 - 08:00
Difficulty: Intermediate
Description: For this 62 residue CASP11 Target, T0779, we are starting you off with 5 different server predictions selected by our WeFold collaborators. Resetting the puzzle will cycle through each model. As this is a small protein, please try out each server start. The topology that initially scores poorly may actually be the closest to the native and could eventually score better than everything else. Conversely, the starting model that scores the best initially, may not get you the most points in the long run!
Categories: CASP11, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 6 days 5 hours ago. Offline
Joined: 05/09/2008
Groups: None
Secondary structure predictions:

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.

Joined: 05/26/2014
Groups: None
foldit

would like to understand a play.as am a pysician of cancer and would like to make a new discovery by tis play..could any one help me ?

Joined: 09/21/2011
Groups: Void Crushers
Why not post this as a symmetry puzzle

As this one is a small dimer why not post it as a dimer? It is small enough for us, and models like number 4 make no sense to explore now.

wisky's picture
User offline. Last seen 8 weeks 2 days ago. Offline
Joined: 07/13/2011
Agreed with Timo.

The CASP11 website says this is a dimer, and it is a very small puzzle. Requesting posted as a dimer, with solutions loadable from previous rounds.

Thank you!

bkoep's picture
User offline. Last seen 1 hour 47 min ago. Offline
Joined: 11/15/2012
Groups: None
Unknown symmetry

This could be an interesting target for a symmetric puzzle, but we should keep in mind that the dimer may not be symmetric. Symmetry is indeed very common in natural protein complexes, but there are plenty of proteins that form non-symmetric oligomers.

Joined: 09/21/2011
Groups: Void Crushers
Very interesting

This would make a very interesting experiment.
Post it as an symmetric dimer and post it as a free dimer.
Also: are the WeFold solutions based on dimer solutions or only on monomers?

And I have the following question:
If it is a non-symmetric dimer I am wondering how the CASP organizors can evaluate how good a solution is.

wisky's picture
User offline. Last seen 8 weeks 2 days ago. Offline
Joined: 07/13/2011
Concur with timo

I totally agree with Timo! I'd like to see it as a symmetric and a non-symmetric dimer :)

KarenCH's picture
User offline. Last seen 43 weeks 5 days ago. Offline
Joined: 07/14/2012
I'd like to see it as a free

I'd like to see it as a free dimer, too. The puzzle as it stands is strange and uninteresting, but I think it'd be much better with two pieces so the interactions between them are easier to see.

Joined: 09/21/2011
would this be possible?

a 5 seg loop with all glyceine that could be placed where we want and this loop could act as a buffer for phobes in the real protein. just something to alter the way the protein responds so that we don't bury phobes that look like a bonding site to another protein. i don't know, i'm just spitballing here.

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