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894: CASP11 T0763: WeFold Round
Status: Closed

Summary

Name: 894: CASP11 T0763: WeFold Round
Status: Closed
Created: 05/16/2014
Points: 100
Expired: 05/22/2014 - 23:59
Difficulty: Intermediate
Description: In this final round for CASP11 Target T0763, we are starting you off with 1 server prediction selected by our WeFold collaborators. Many more details in the puzzle comments.
Categories: CASP11, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 7 hours 49 min ago. Offline
Joined: 05/09/2008
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More details

Since this is a big and nasty CASP target, we're giving you just one server model to work on this time... hopefully this helps reduce the crashes with this target.

Here is a link to the previous round of this puzzle, with SS predictions and more:
https://fold.it/portal/node/997647#comment-27591

Joined: 09/21/2011
Changing server prediction

This has a section that is either bad, or its a binding site; not sure which. On such a large protein, is it useful to make major changes that I know will score better, but i have no real expectation that it is more accurate, or should I stick with the general arrangement and make modifications where I see potential problems?

beta_helix's picture
User offline. Last seen 7 hours 49 min ago. Offline
Joined: 05/09/2008
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On this particularly difficult target, feel free to change it

Great question, karstenw!

The CASP organizers had already posted this one as a CASP ROLL target last year:
http://predictioncenter.org/casprol/target.cgi?id=88
=
http://predictioncenter.org/casp11/target.cgi?id=8

(Maybe it looked a bit familiar: https://fold.it/portal/node/996451 :-)

but I think it’s such an interesting one that they wanted the human CASP11 groups to take a stab at it.

They already told us that it’s a dimer (which they hadn’t mentioned in CASP ROLL) and check out the trans-membrane prediction:

Because of all of this, our confidence in this server model is quite low, so you should feel free to try very drastic topological changes (rather than just trying to find the top-scoring conformation closest to the starting structure).

spmm's picture
User offline. Last seen 41 weeks 3 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
scoring of different topologies

So even if we create a solution with a different topology when we know the native is a dimer, we have little chance of making it score in CASP or foldit unless we get the other part, assuming you can work out what the sym is?

bkoep's picture
User offline. Last seen 3 hours 29 min ago. Offline
Joined: 11/15/2012
Groups: None
No need to worry

I'm not entirely sure what you're getting at, but maybe this will help:

Some of the targets in CASP are known to self-associate (form dimers, trimers, etc.), and CASP provides this information so that it might help you predict the structure of the monomer. However, it is not necessary to predict the structure of the full multimer. For example, for target T0763, CASP assessors will compare your monomer prediction with a single subunit of the dimer. Some groups may also submit predictions for the full dimer, but those predictions will be evaluated separately.

If we knew the symmetry of the dimer, we would run this target as a symmetry puzzle.

spmm's picture
User offline. Last seen 41 weeks 3 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
tx

hopefully it is not like 3ks7 which would be a lovely sym puzzle :D

beta_helix's picture
User offline. Last seen 7 hours 49 min ago. Offline
Joined: 05/09/2008
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397 residues?

In CASP10 we were fortunate to correctly guess the symmetry of one of the refinement targets (TR722), so we were able to post it as a symmetry puzzle: http://fold.it/portal/node/993251#comment-19148

It was this target that our WeFold collaborators were able to pick out and improve one of your Foldit predictions, resulting in the best CASP submission for that target (wfFUIK): http://fold.it/portal/files/Slide2.png

So, if for any CASP11 targets you are find some evidence of symmetry, please do let us know!

But I don't know if everyone would agree that a 397 symmetry puzzle would be lovely :-P
http://www.pdb.org/pdb/explore/explore.do?structureId=3KS7

wisky's picture
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Joined: 07/13/2011
...

My eyes... they burn....

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