611: CASP10 Refinement Puzzle: TR752

Closed since over 13 years ago

Summary

• Created: August 02, 2012
• Expires: August 10, 2012 at 15:00 UTC
• Max points: 100

Description

This is the twenty-first CASP10 Refinement Target. This model was the best server prediction for target T0752, generated by the BAKER-ROSETTASERVER (using Rosetta@home). We've been told that ~90% of this model matches the native! So (for once) you won't need to change the starting model much. In addition, the organizers have given us "Special attention regions: 41-50, 100-110, 125-128." These are highlighted in Note Mode.

Top groups

• 21. DSN @ Home 1 pt. 11,224

Top soloists

• 71. greepski 10 pts. 11,842
• 72. abiogenesis 9 pts. 11,840
• 73. Ssle 9 pts. 11,836
• 74. Aubade00 9 pts. 11,832
• 75. Merf 8 pts. 11,817
• 76. spmm 8 pts. 11,815
• 77. DrMistry 8 pts. 11,814
• 78. ComputerMage 7 pts. 11,813
• 79. jogie62 7 pts. 11,811
• 80. weitzen 7 pts. 11,810

Comments

[beta_helix]

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

We recommend focusing your work on these 3 regions.

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This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=203

The CASP10 organizers gave us this hint:

"Starting model GDT_TS=90. Special attention regions: 41-50, 100-110, 125-128."

GDT_TS=90 essentially means that 90% of the model superimposes correctly onto the native structure:

en.wikipedia.org

Global distance test

The global distance test (GDT), also written as GDT_TS to represent "total score", is a measure of similarity between two protein structures with known amino acid correspondences (e.g. identical amino acid sequences) but different tertiary structures. It is most commonly used to compare the results of protein structure prediction to the experimentally determined structure as measured by X-ray crystallography, protein NMR, or, increasingly, cryoelectron microscopy. The metric was developed by Ada...

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 80-81, 94, 114-115, 123 & 134 are highly predicted to be part of a sheet. However, the Valines at residues 45, 52 & 103 are predicted to be in anything.