puzzle picture
678: Large CASP ROLL Target R0027 with symmetry
Status: Closed


Name: 678: Large CASP ROLL Target R0027 with symmetry
Status: Closed
Created: 02/15/2013
Points: 100
Expired: 02/27/2013 - 13:00
Difficulty: Advanced
Description: This one is going to be tough! Again the CASP organizers have told us that this "protein is known to form very stable homo-trimers", so we are again giving you the 5 RosettaServer models for R0027 with symmetry. Resetting the puzzle will cycle through the 5 different server predictions (as well as an extended conformation). More details about this CASP target are in the puzzle comments.
Categories: CASP ROLL, Overall, Prediction, Symmetry

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beta_helix's picture
User offline. Last seen 2 days 7 min ago. Offline
Joined: 05/09/2008
Groups: None
More details:

This target was already large enough as a monomer, that we realize how difficult this will be as a trimer.

We have trimmed the first 11 residues, based on a disorder prediction (http://prdos.hgc.jp/cgi-bin/meta/result.cgi?ppid=146304p1d1360963642) to try to make this puzzle a bit more manageable.

The original Secondary Structure Information (for the full sequence) and the link to the CASP target is here: http://fold.it/portal/node/994456#comment-21574

gramps's picture
User offline. Last seen 7 years 51 weeks ago. Offline
Joined: 12/16/2010
Select Best Start analyisis

output of public ...
Recipe: Rav3n_pl SBS v1.2

Saving in slot 1 start points: -6879.1552140217
Saving in slot 2 start points: 16343.670764804
Saving in slot 3 start points: 16413.019633088
Saving in slot 4 start points: 8955.3068776678
Saving in slot 5 start points: 15615.134722876
Saving in slot 6 start points: -21324.46323487
Found 6 starts. Searching for best.
Save 1 start points: -6879.1552140217
Stabilzed, fuzed and saved at: 15712.551110252
Save 2 start points: 16343.670764804
Stabilzed, fuzed and saved at: 17837.785759885
Save 3 start points: 16413.019633088
Stabilzed, fuzed and saved at: 17784.967177499
Save 4 start points: 8955.3068776678
Stabilzed, fuzed and saved at: 16756.193075522
Save 5 start points: 15615.134722876
Stabilzed, fuzed and saved at: 17174.954751309
Save 6 start points: -21324.46323487
Stabilzed, fuzed and saved at: 6387.2909714933
Restoring best score. Happy folding ;]

With interpretation:

Structure 1 start points: -6879.155
Stabilzed, fuzed and saved at: 15712.551

Structure 2 start points: 16343.670
Stabilzed, fuzed and saved at: 17837.785

Structure 3 start points: 16413.019
Stabilzed, fuzed and saved at: 17784.967

Structure 4 start points: 8955.306
Stabilzed, fuzed and saved at: 16756.193

Structure 5 start points: 15615.134
Stabilzed, fuzed and saved at: 17174.954

Structure 6 start points: -21324.463 -- extended chain
Stabilzed, fuzed and saved at: 6387.290

Your mileage may vary, to visit the six saves after your SBS run consider public ...
Recipe: Quicksave extend V1.0

Use the "load" slider to visit desired start.

The following can be used to load "first draft" structs onto the models (the AAs are the same as 674 but with the first, N-end, 11 segs removed, so adapting the 674 data to this puzzle involved some manual work, transcription errors are possible):

Recipe: 678 jpred structs

Recipe: 678 comment structs

This recipe can be used to help save further manual edits of the structs:

Recipe: autogen structure code V1

Hopefully the above is clear enough that I don't need to rehearse this procedure again in future puzzles of this type ;-)

Joined: 08/24/2011
WAY too large!

beta_helix: "This CASP ROLL target might be too large for symmetry

Indeed, Jean-Bob... if this puzzle is already quite slow as a monomer, it might not be feasible as a trimer! :-("

R0026 was already too slow on its symmetry version, why this puzzle? I mean that's what? 5 puzzles I can barely "play" with? A mere shake lasts at least a minute, where's the fun? And when the puzzles are "fast", they're posted in a crazy hurry and they come with the wrong settings so we must start again and lose hours of work (thrice in a month?!)

I'm begging you, please give us the fun back, as of now I'm feeling kicked out from this wonderful project.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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