605: CASP10 Refinement Puzzle: TR710

Closed since over 13 years ago

Summary

• Created: July 23, 2012
• Expires: August 02, 2012 at 23:59 UTC
• Max points: 100

Description

This is the fifteenth CASP10 Refinement Target. We've been told that about 75% of this model matches the native, so you'll need to refine ~25% of the structure! More info in the puzzle comments.

Top groups

• 21. Czech National Team 1 pt. 12,353
• 22. Skeptics Guide to the Universe 1 pt. 12,264
• 23. Friday Lab 1 pt. 12,179
• 24. DSN @ Home 1 pt. 12,149

Top soloists

• 61. weitzen 21 pts. 12,827
• 62. BootsMcGraw 20 pts. 12,826
• 63. Tyggy Too 19 pts. 12,826
• 64. TheGUmmer 19 pts. 12,824
• 65. Psych0Active 18 pts. 12,824
• 66. CheezWhiz 18 pts. 12,824
• 67. drumpeter18yrs9yrs 17 pts. 12,820
• 68. Deleted player pts. 12,820
• 69. Deleted player pts. 12,818
• 70. abiogenesis 16 pts. 12,815

Comments

[beta_helix]

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=188

The CASP10 organizers gave us this hint:

"Starting model GDT_TS=75."

GDT_TS=75 essentially means that 75% 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 19, 52, 85, 145 & 177 are highly predicted to be part of a helix. However, the Valines at residues 96 & 100 are not.