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606: Large CASP10 Refinement Puzzle: TR708
Status: Closed

Summary

Name: 606: Large CASP10 Refinement Puzzle: TR708
Status: Closed
Created: 07/24/2012
Points: 100
Expired: 08/05/2012 - 08:00
Difficulty: Advanced
Description: The sixteenth CASP10 Refinement Target has 196 residues! This model was the best server prediction for target T0708, generated by the MULTICOM server. We've been told that ~86% of this model matches the native, so you just need to find which 14% to refine! We are giving you extra time to work on this one due to its size. More info in the puzzle comments.
Categories: CASP10, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 4 days 15 hours ago. Offline
Joined: 05/09/2008
Groups: None
More info here:

Please note that the Cut Tool is available on this puzzle!

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=190

The CASP10 organizers gave us this hint:

"Starting model GDT_TS=86."

GDT_TS=86 essentially means that 86% 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 Valines at residues 48, 140 & 168 are highly predicted to be part of a helix. However, the Valines at residues 68, 99, 127 & 153 are predicted to be part of a sheet.

gramps's picture
User offline. Last seen 5 years 1 day ago. Offline
Joined: 12/16/2010
let's talk about the C-end

From the initial pose of this puzzle, after changing the structures to match (more or less) the predicted structures it's apparent that the high seg end (C-end) has a pose that doesn't match the predicted structures.

ADVERTISEMENT: ;-)
consider the new ScriptV2 version of my "autogen structure code V1" as an aid for saving and sharing changed structure codes, e.g. when the predicted structures differ a lot from the initial structures as they do here.
http://fold.it/portal/recipe/43480

beta_helix's picture
User offline. Last seen 4 days 15 hours ago. Offline
Joined: 05/09/2008
Groups: None
As pointed out here

As pointed out here (http://fold.it/portal/node/993286) the above image has disappeared!

It can be found here:
http://fold.it/portal/files/images/seqLogo_46.thumbnail.png

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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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