582: Beginner CASP10 Refinement Puzzle: TR674

Closed since almost 14 years ago

Summary

• Created: June 22, 2012
• Expires: June 30, 2012 at 02:00 UTC
• Max points: 100

Description

This is the sixth CASP10 Refinement Target. This model was the best human prediction for target T0674. We've been told that ~84% of this model matches the native, so you just need to find which 16% to refine! More info in the puzzle comments.

Top groups

• 31. Deleted group pts. 8,369

Top soloists

• 181. bojler 1 pt. 10,896
• 182. abiogenesis 1 pt. 10,890
• 183. al_ 1 pt. 10,890
• 184. crpainter 1 pt. 10,879
• 185. Schnecke 1 pt. 10,879
• 186. JayArrgh 1 pt. 10,870
• 187. Arne Heessels 1 pt. 10,863
• 188. RandyFithian 1 pt. 10,858
• 189. monkry 1 pt. 10,857
• 190. deLaCeiba 1 pt. 10,852

Comments

[beta_helix]

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=131&view=refinement

Note that the organizers gave us this hint:

"Starting model GDT_TS=84."

GDT_TS=84 essentially means that 84% 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...

Secondary Structure Predictions below:

[beta_helix]

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 10, 12 & 45 are highly predicted to be part of a helix. However, the Valine at residue 93 is predicted to be in a sheet.