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613: CASP10 Refinement Puzzle: TR655
Status: Closed

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RankGroupScorePoints
1foldeRNA12,541100
2Anthropic Dreams12,52981
3Contenders12,45065
4Void Crushers12,35251
5Beta Folders12,33840
6Go Science12,26031
7L'Alliance Francophone12,25024
8Russian team12,18918
9FoldIt@Netherlands12,14614
10Team Hungary11,84810
11Natural Abilities11,8148
12SETI.Germany11,5296
13Brony@Home11,4094
14Gargleblasters11,4013
15Geekdo10,8662
16Newton's Cradle10,3202
17Freedom Folders10,1931
18xkcd10,1701
19Another Hour Another Point10,1611
20Piratenpartei Deutschland10,0001
21hhv99,7161
22Crunching Family9,6871
23Team Canada9,6851
24SETIKAH@KOREA9,6491
25Czech National Team9,5471


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Comments

beta_helix's picture
User offline. Last seen 2 days 4 hours ago. Offline
Joined: 05/09/2008
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More info here:

Please look at the Notes for this puzzle (by pressing 3 in the Original Interface, or pressing 1 in the Selection Interface).

************

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=212

The CASP10 organizers gave us this hint:

"The experimental NMR structure shows quite a bit of disorder in regions 91-93 and 142-163. Regions 6-20 and 51-64 need special attention. Starting model GDT_TS=69 (including the internal disordered regions)."

GDT_TS=69 essentially means that 69% of the model superimposes correctly onto the native structure:
http://en.wikipedia.org/wiki/Global_distance_test

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.

For example, the Valine at residue 92 is highly predicted to be part of a sheet. However, the Valine at residue 92 is predicted to be in a helix.

Joined: 05/19/2009
Groups: Contenders
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At the moment of writing, this puzzle is not visible in either main or devprev.

brow42's picture
User offline. Last seen 3 weeks 2 hours ago. Offline
Joined: 09/19/2011
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It's there now 8:00 PDT 15:00

It's there now 8:00 PDT 15:00 GMT.

Susume's picture
User offline. Last seen 13 hours 58 min ago. Offline
Joined: 10/02/2011
"Disorder" is not clear to me

"Disorder" is not clear to me - does that mean those areas will not be scored for CASP so it doesn't matter if we move them?

beta_helix's picture
User offline. Last seen 2 days 4 hours ago. Offline
Joined: 05/09/2008
Groups: None
They haven't been very clear on this.

Normally, disordered regions will not be scored.
See TR754 as an example:
http://predictioncenter.org/casp10/target.cgi?id=211&view=refinement
"Residues 1-8 and 77-80 are disordered in the experimental structure and deleted from the model."

It probably means that they will simply ignore that region (but you never know... they have never mentioned this sort of thing in previous CASPs), I would just not worry about those regions and focus on Regions 6-20 and 51-64.

Sequence Logo can be found here (since it keeps vanishing):
http://fold.it/portal/files/images/seqLogo_52.png

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