puzzle picture
630: Quick Frozen Cutpoint Puzzle
Status: Closed


Name: 630: Quick Frozen Cutpoint Puzzle
Status: Closed
Created: 09/14/2012
Points: 100
Expired: 09/20/2012 - 20:00
Difficulty: Beginner
Description: We want to try out a very different kind of puzzle. The entire protein has been locked, and we need you to fit the pieces of this puzzle in the correct way. NOTE: CUTPOINTS CANNOT BE CLOSED FOR THIS PUZZLE. Have fun with this one! More details of why this type of puzzle could be useful in the comments.
Categories: Overall, Prediction

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beta_helix's picture
User offline. Last seen 8 hours 26 min ago. Offline
Joined: 05/09/2008
Groups: None
Why this crazy puzzle?!

You might be wondering how such a puzzle could be useful.

As many of you noticed during CASP10 when using the alignment tool, certain regions of the target sequence aligned very well (across all the different templates).
For example: perhaps all the templates had a helix when threading residues 1-30 for a particular target, but after residue 31 all the templates had very different topologies.

This is where freezing the N-terminal helix might be useful. In cases where the homology to known solved templates is very strong, we might want to use that exact structure and not let Rosetta wiggle it out of that conformation... instead letting you focus on the other regions.

To an extend we've tried using constraints for this, but often constraints make folding a lot more difficult. We'd like to see how you do with frozen regions.

Good luck and have fun... at least you don't need any secondary structure predictions!

Joined: 08/24/2011
Groups: Go Science
Need a "group" command

So one thing I've already noticed: it's OK if we're not allowed to close the cutpoints, but if that's the case, the move tool needs to be able to select and move multiple pieces at once. Otherwise, I can arrange three or four pieces in a way I like, then around a few other pieces in a way I like, and I can't move the groups together without disturbing the arrangement.

spmm's picture
User offline. Last seen 18 weeks 1 day ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
great post tutorial puzzle

This would be a great puzzle for learning how sheets bond and about loops etc maybe it could be a long running contest for people to learn on. Fewer distractions and the sheets don't bend :) Also forces practice with the move tools.

beta_helix's picture
User offline. Last seen 8 hours 26 min ago. Offline
Joined: 05/09/2008
Groups: None
Thank you for the feedback, spmm

I know there have been a lot of suggestions on how to improve this puzzle (which is expected, since it's the first time we've ever posted anything like this).
Do you think it would be a decent Intro Puzzle (perhaps just after the Move Tool intro: Puzzle 5-2) in it's current state, or we need to tweak it a little more so that it's not too frustrating?

Thanks again for the great suggestion.

The idea of posting previous Science Puzzles as Intro Levels has been brought up often (perhaps having them be in between the Intro Levels and the Science Puzzles) so knowing which puzzles would be useful for this is very helpful!

Perhaps we should start a Forum post about it (similar to the "which is the most useful Beginner Puzzle?" thread).

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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, Boehringer Ingelheim, RosettaCommons