puzzle picture
657: Blind Electron Density 3
Status: Closed

Summary

Name: 657: Blind Electron Density 3
Status: Closed
Created: 11/27/2012
Points: 100
Expired: 12/04/2012 - 23:00
Difficulty: Advanced
Description: This is our third electron density puzzle with real data. Like our second puzzle, we were able to pinpoint which regions belong to a single copy. Try to fit the protein into the density to get the best score!
Categories: Electron Density, Overall, Prediction

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Comments

jflat06's picture
User offline. Last seen 5 days 3 hours ago. Offline
Joined: 09/29/2010
Groups: Window Group
JPRED Secondary Structure Predictions

You can find secondary structure predictions from Jpred here:

http://fold.it/portal/node/993971

steveB's picture
User offline. Last seen 2 years 43 weeks ago. Offline
Joined: 01/08/2009
Groups: Void Crushers
Data quantity

There appears to be less detail in the ED mesh on this puzzle, or you have changed the programme slightly. The threshold slider on this puzzle is best set to maximum, ie as far to the left as possible

jflat06's picture
User offline. Last seen 5 days 3 hours ago. Offline
Joined: 09/29/2010
Groups: Window Group
.

The density quality will vary from protein to protein, as the resolution of the data gathered from the experimental methods isn't always the same.

steveB's picture
User offline. Last seen 2 years 43 weeks ago. Offline
Joined: 01/08/2009
Groups: Void Crushers
128 Mb data limit

I understand from Brow42 that the first posting of this puzzle didn't work because the ED data exceeded 128 Mb. Was there any data loss in re-issuing the puzzle with a smaller data file ?

jflat06's picture
User offline. Last seen 5 days 3 hours ago. Offline
Joined: 09/29/2010
Groups: Window Group
.

The original puzzle was posted as an untrimmed case, where the entire density cell was included (including the extraneous bits of density from other copies).

We decided to repost the puzzle as the trimmed case, as the density is smaller. I believe what was lost was only the extra bits of density, and not any of the resolution.

The trimmed case isn't 100% blind, as we decided what to trim based on the actual solved structure - however, in these last 2 cases, the trimming could very feasibly be done without knowledge of the structure, so it's still a very cool result.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons