610: CASP10 Refinement Puzzle: TR750

Closed since over 13 years ago

Summary

• Created: August 01, 2012
• Expires: August 11, 2012 at 03:00 UTC
• Max points: 100

Description

This is the twentieth CASP10 Refinement Target. We've been told that ~77% of this model matches the native, so you'll need to refine ~23% of the structure! More info in the puzzle comments.

Top groups

• 1. Anthropic Dreams 100 pts. 12,384
• 2. foldeRNA 80 pts. 12,333
• 3. Go Science 63 pts. 12,321
• 4. Beta Folders 49 pts. 12,317
• 5. Void Crushers 37 pts. 12,271
• 6. Contenders 28 pts. 12,184
• 7. L'Alliance Francophone 21 pts. 12,179
• 8. FoldIt@Netherlands 15 pts. 12,177
• 9. Deleted group pts. 12,166
• 10. Russian team 8 pts. 12,063

Top soloists

• 161. nmos1056 1 pt. 10,958
• 162. twisted1 1 pt. 10,946
• 163. jellyarren 1 pt. 10,932
• 164. Tac1 1 pt. 10,924
• 165. ten_string 1 pt. 10,916
• 166. lamoille 1 pt. 10,912
• 167. Bearpaw 1 pt. 10,911
• 168. lb494 1 pt. 10,904
• 169. mirjamvandelft 1 pt. 10,895
• 170. Vie 1 pt. 10,866

Comments

[beta_helix]

Please note that the Cut Tool is available on all puzzles from now on!

This is the page for this CASP10 refinement target:
http://predictioncenter.org/casp10/target.cgi?id=202

The CASP10 organizers gave us this hint:

"Starting model GDT_TS=77."

GDT_TS=77 essentially means that 77% 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 84 & 176 are highly predicted to be part of a helix. However, the Valines at residues 64-65 & 99 are predicted to be part of a sheet.