662: Blind Electron Density 4

Summary

Name:

Status:

Closed

Created:

12/20/2012

Points:

100

Expired:

01/05/2013 - 08:00

Difficulty:

Advanced

Description:

This is our fourth electron density puzzle with real data. Like our previous puzzles, we were able to pinpoint which regions belong to a single copy, though the density itself is less clear. Try to fit the protein into the density to get the best score! Secondary Structure Predictions are posted in the puzzle comments.

Categories:

Electron Density, Overall, Prediction

Rank

Group

Score

Points

Anthropic Dreams

5,313

100

5,025

4,991

2,711

1,979

Rank

Player

Group

Score

Points

Galaxie 4 9

Anthropic Dreams

5,296

100

5,240

5,212

5,209

5,203

Rank

Player

Group

Score

Points

karstenw 93 2664

Anthropic Dreams

5,313

100

5,176

5,025

4,991

4,836

Fri, 12/21/2012 - 02:16

beta_helix 93 2664

Offline

Joined: 05/09/2008

Groups: None

Secondary structure predictions:

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 amino acid Leucine at residue 37 is highly predicted to be part of a sheet. However, the Valines at residues 6-7 & 97 have an equal probability of being anything.

Wed, 12/26/2012 - 21:03

bertro 93 2664

Offline

Joined: 05/02/2011

Groups: Beta Folders

Smoother and Cleaner Density Cloud possible?

I believe it is possible to improve this density cloud clarity:

1) The current density map seems to have been saved with a step of 2 (judging by the rough angles of the blobs) giving us a much rougher image to work with than with a step of 1.

2) Plus some dust cleaning (removing small blobs) would also greatly enhance our ability to navigate and distinguish the shape of the protein.

Please, could you re-submit the puzzle with a smoother/cleaner density cloud?

Thanks