puzzle picture
746: R0034 with Electron Density: Round 1
Status: Closed

Summary

Name: 746: R0034 with Electron Density: Round 1
Status: Closed
Created: 07/15/2013
Points: 100
Expired: 07/23/2013 - 02:00
Difficulty: Advanced
Description: This Electron Density puzzle is going to be as hard as it gets, which is why we are splitting it into 2 rounds. For this round, we have not trimmed the density. Again, the automated methods were unable to solve this structure using this huge density cloud. We will trim this density in Round 2 based on your top-scoring solutions for this round! Unfortunately there are no available templates to start with for this puzzle, so you'll have to use all your Electron Density folding skills to fit the density as well as you can! The secondary structure predictions have been loaded onto the starting model, with more details posted in the puzzle comments.
Categories: CASP ROLL, Electron Density, Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 1 day 3 hours ago. Offline
Joined: 05/09/2008
Groups: None
More details:

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 7, 43, 68 and 89 is highly predicted to be part of a helix. However, the Valine at residue 100 is not predicted to be anything!

The above predictions are already on the starting model (based on the horizontal lines in the above figure).

__________________________________________

Cutaway view hint:
If you hover your mouse over a segment and type shift-Q, the game will hide parts of the protein and cloud that are not in the same plane as that segment - it cuts down on how much cloud you see at one time and makes it easier to focus. Q returns to normal view.
__________________________________________

New Electron Density Features:

- Notes can be added to the electron density if present. To add one, press TAB with the mouse over the density while the density panel is open. Use the recycle button in the note panel to erase one. (Note: saving and sharing these notes is a feature that should be in a future release)

There is a video on our YouTube channel explaining how to add Notes to the electron density

- There is a button in the Electron Density Panel to focus rotation on the density. You can use the HOME or Q keys to refocus on the protein.
- The density score of a residue may now be viewed in the tab menu
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We are unable to let you load in your solutions from previous CASP ROLL R0034 Puzzles, because the sequence has been trimmed (due to the electron density) compared to the previous puzzles.

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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