puzzle picture
422: De-novo Freestyle 7
Status: Closed

Summary

Name: 422: De-novo Freestyle 7
Status: Closed
Created: 05/21/2011
Points: 100
Expired: 05/28/2011 - 17:00
Difficulty: Advanced
Description: We are giving you this currently unsolved protein as an extended chain. Use all your skills to fold it up as best as you can. The secondary structure predictions are posted in the puzzle comments, but we have included them in the starting structure as well.
Categories: Overall, Prediction

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Comments

beta_helix's picture
User offline. Last seen 21 hours 36 min ago. Offline
Joined: 05/09/2008
Groups: None
Please try to use these secondary structure predictions:

As requested in the feedback, http://fold.it/portal/node/989298 these secondary structure predictions have been pre-loaded into this freestyle puzzle.

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 20 is highly predicted to be part of a helix. However, the Leucine at residue 16 is equally predicted to be anything.

Joined: 01/19/2011
trouble loading

Why can't I see this in my list of puzzles?
Really want to get to work on this one...

beta_helix's picture
User offline. Last seen 21 hours 36 min ago. Offline
Joined: 05/09/2008
Groups: None
should be up now!

Enjoy!

spvincent's picture
User offline. Last seen 51 min 48 sec ago. Offline
Joined: 12/07/2007
Groups: Contenders
One thing I've noticed in the

One thing I've noticed in the high-scoring solutions I've seen for these de novo puzzles is that any sheets tend to be unnaturally straight. In real-world proteins (see the recently-completed 419 as an example) sheets are usually curved, but this is difficult to achieve in FoldIt, particularly when one starts with a perfectly straight sheet as happens in these puzzles.

A personal preference this; but I think trying to fold from a totally unfolded protein is too purist an approach. I'd rather have a few random Rosetta@home predictions to start from (you could use them to populate the Alignment tool).

bendbob's picture
User offline. Last seen 15 weeks 3 days ago. Offline
Joined: 05/06/2011
How to get SS details?

I do not know about getting serve data for SS's. Any pointers and clues are appreciated.

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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