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450: Huge Unsolved Leishmania Parasite Protein
Status: Closed

Summary

Name: 450: Huge Unsolved Leishmania Parasite Protein
Status: Closed
Created: 08/25/2011
Points: 200
Expired: 09/16/2011 - 23:59
Difficulty: Advanced
Description: This one's going to be tough. Every attempt so far to solve this 244-residue protein has failed. There are no NMR models to use as starting points, so we are giving you 5 Zhang Server predictions to start from. Each time you reset the puzzle one of these 5 models will randomly be chosen. They are also in the Alignment Tool so you can use partial threading. Since this protein is so big we are giving you 20 days to work on it (for 200 global points) and we'll post as much help as we can in the puzzle comments.
Categories: Overall, Prediction

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1Anthropic Dreams14,025200
2Void Crushers13,797154
3Contenders13,773117
4foldeRNA13,65388
5Go Science13,41566

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Comments

beta_helix's picture
User offline. Last seen 5 days 16 hours ago. Offline
Joined: 05/09/2008
Groups: None
We realize this will not be easy...

but due to Foldit's success with the previously unsolved monkey virus protein (http://fold.it/portal/node/989012) we wanted to let you try out this big protein since every other method to solve it has failed.

Here are some tips to help your computer run Foldit faster:

After opening this puzzle for the first time (before even shaking or wiggling)
go to View and turn off "Show sidechains with clashes or exposeds"
Under View Sidechains: select "Don't Show (Fast)"
Turn off everything under View Options (especially "Show Clashes")

If you selected "Show Advanced GUI"
(available under the Menu->General Options button) then in the View Menu turn on "Fade GUI" (or even "Hide GUI" at times if you don't need it) and when you plan to run something for a while (even just shake or wiggle) select "Line" under View Protein. Then set it back to Cartoon when you want to manipulate the protein again.

Foldit can run faster if it doesn't have as much graphics to render, so when running recipes (or long wiggles/shakes) you can move the protein off of the screen (and get it back by pressing Q) and if you are on PC you can minimize the Foldit application to your taskbar and it won't render the graphics.

This puzzle will be tough, but once you get rid of the clashes (don't forget to use the Behavior Tab) you should be able to manipulate it.

Please post any other speedups that you know of!
Thanks and good luck!

Joined: 06/17/2010
SBS results

I takes over 2.5 hours but:

Save 1 start points: -35170.683355334 - model 2
Stabilzed, fuzed and saved at: 11441.483779276
Save 2 start points: -35411.111519259 - model 3
Stabilzed, fuzed and saved at: 10998.760213389
Save 3 start points: -26984.75861465 - model 4
Stabilzed, fuzed and saved at: 11180.802313728
Save 4 start points: -67135.737279717 - model 5
Stabilzed, fuzed and saved at: 11487.285480836
Save 5 start points: -39946.359775718 - model 1
Stabilzed, fuzed and saved at: 11856.137023034

Looks like model 1 is scoring best at start.

beta_helix's picture
User offline. Last seen 5 days 16 hours ago. Offline
Joined: 05/09/2008
Groups: None
Additional info about this protein:

This is the unsolved protein:
http://www.ncbi.nlm.nih.gov/protein/76363613?report=genbank&log$=protalign&blast_rank=1&RID=5K54MX9Z01S

Not much info about it, but luckily there is a homologous solved structure: 2pxx (http://www.rcsb.org/pdb/explore/explore.do?structureId=2pxx) it just wasn't close enough to solve the structure using Molecular Replacement.

You can see how that homolog was used by the Zhang Server for its 5 predictions (you'll also find secondary structure predictions, hydrophobicity predictions, different alignments to 2pxx and more) here: http://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S79415/

Lastly, below are the secondary structure predictions (in sequence logo form) from the SAM-T08 server (since they don't agree perfectly with the Zhang server secondary structure predictions):

gramps's picture
User offline. Last seen 5 years 20 weeks ago. Offline
Joined: 12/16/2010
Skype on standby a problem?

This may be coincidence but I've recently found the setting to prevent Skype from starting up in the background when I log in, and recipe performance seems to have become friskier since (Win7). In general it's probably better to have as little other major S/W running as possible when folding, but I just have a feeling that Skype in particular is a real hog. Presumably things like streaming video and such would also affect folding performance.

rws's picture
User offline. Last seen 3 years 44 weeks ago. Offline
Joined: 08/13/2008
Groups: SETI.Germany
another model / sec. structure

another model and predictions for this protein is at SWISS MODEL:
http://swissmodel.expasy.org/repository/smr.php?sptr_ac=Q95Z88&csm=EDAA56F1FB3D50C7

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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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