puzzle picture
412: Electron Density Trace Puzzle
Status: Closed


Name: 412: Electron Density Trace Puzzle
Status: Closed
Created: 04/15/2011
Points: 100
Expired: 04/23/2011 - 23:00
Difficulty: Intermediate
Description: This Rosetta model was generated by trying to fit an electron density map, but as you can see the resulting trace looks pretty bad. We have tried various Rosetta protocols on this model but they aren't able to make it look any better, so we are hoping your human skills can spot what areas need to be improved the most.
Categories: Overall, Prediction

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Joined: 06/17/2010
Our goal is

to optimize it or make own folds?
Make totally fifferent aligement or "just" optimize existing one?

Joined: 02/23/2011
AA are probably where they should be?

I looked up Electron Density Trace and I got the impression that the method predicts where each AA probably is with some margin for error. So, does that mean we should try not to change their locations too much? Is there any chance you can show us the original results with the probabilities?

beta_helix's picture
User offline. Last seen 3 days 13 hours ago. Offline
Joined: 05/09/2008
Groups: None
thanks for asking!

Indeed, the data indicates that this model is close to the native geometrically but you can see that it needs a lot of work and optimization.

So drastic restructuring moves should not be necessary, but finding the native low-energy well should still be a challenge!

I will see if we can provide you with some of the experimental data, if not on this puzzle we can try it with future 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