puzzle picture
1120: Unsolved De-novo Freestyle 54
Status: Closed

Summary

Name: 1120: Unsolved De-novo Freestyle 54
Status: Closed
Created: 07/30/2015
Points: 100
Expired: 08/06/2015 - 23:00
Difficulty: Intermediate
Description: The structure of this protein is still unsolved. The PSIPRED secondary structure predictions are provided on the starting model.

Sequence:
MQTLTVADFALRLAVGVGCGAIIGLERQWRARMAGLRTNALVATGATLFVLYAVATEDSSPTRVASYVVSGIGFLGGGVILREGFNVRGLNTAATLWCSAAVGVLAASGHLVFTLIGTGTIVAVHLLGRPLGRLVDRDNA
Categories: Overall, Prediction

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Comments

Madde's picture
User offline. Last seen 19 weeks 1 day ago. Offline
Joined: 05/29/2008
Groups: Void Crushers
Jpred4 predictions

For the next two days you can see the secondary structure prediction of the Jpred 4 server at
http://www.compbio.dundee.ac.uk/jpred4/results/jp_cdjyugd/jp_cdjyugd.results.html

bkoep's picture
User offline. Last seen 12 hours 30 min ago. Offline
Joined: 11/15/2012
Groups: None
Better predictions

These secondary structure predictions are probably more accurate than those provided on the starting solution. It seems there was a problem with our original PSIPRED predictions for this sequence.

Thanks Madde!

Madde's picture
User offline. Last seen 19 weeks 1 day ago. Offline
Joined: 05/29/2008
Groups: Void Crushers
Simplified version of the Jpred4 SS prediction
































See http://fold.it/portal/node/2001002 for a colorized version of the picture above

Joined: 12/29/2013
Groups: Beta Folders
thank you for sharing this

thank you for sharing this

Madde's picture
User offline. Last seen 19 weeks 1 day ago. Offline
Joined: 05/29/2008
Groups: Void Crushers
Psipred prediction
Joined: 07/21/2013
Groups: Beta Folders
format of the Jpred4 SS prediction

the display of the
Simplified version of the Jpred4 SS prediction
above was as a JPG file. Could you display it
as plain text? That way, a player could copy the
text string an put it in a "set the amino acids"
program?

Madde's picture
User offline. Last seen 19 weeks 1 day ago. Offline
Joined: 05/29/2008
Groups: Void Crushers
Jpred4 prediction as plain text

1---------11--------21--------31--------41--------51--------61--------71--------81--------91--------101-------111-------121-------131-------
MQTLTVADFALRLAVGVGCGAIIGLERQWRARMAGLRTNALVATGATLFVLYAVATEDSSPTRVASYVVSGIGFLGGGVILREGFNVRGLNTAATLWCSAAVGVLAASGHLVFTLIGTGTIVAVHLLGRPLGRLVDRDNA
CCCCcHHHHHHHHHHHHHHHHHHhhcchhccCCCccHHHHHHHHHHHHHHHHHHhccCCCCchHHHHHHHHHHHhhhcceeecCcceechhhhhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHhHHHHHHHccCCC
99972799999999999999999200111047776378999999999999999812688876278999999987330212231763210130358999999999874201589999999999999885899998715999

Joined: 07/21/2013
Groups: Beta Folders
nice plain text

Danke

Joined: 07/21/2013
Groups: Beta Folders
nice plain text

Danke

Batz's picture
User offline. Last seen 23 hours 49 min ago. Offline
Joined: 02/16/2012
Groups: Go Science
Membrane Protein?

Maybe too late, but the OCTOPUS server predicted this protein to be a membrane protein...
You should maybe add this into the description.

Sequence name: query_sequence
Sequence length: 140 aa.
Sequence:
MQTLTVADFALRLAVGVGCGAIIGLERQWRARMAGLRTNALVATGATLFVLYAVATEDSS
PTRVASYVVSGIGFLGGGVILREGFNVRGLNTAATLWCSAAVGVLAASGHLVFTLIGTGT
IVAVHLLGRPLGRLVDRDNA

SPOCTOPUS predicted topology:
ooooMMMMMMMMMMMMMMMMMMMMMiiiiiiiiMMMMMMMMMMMMMMMMMMMMMoooooo
ooMMMMMMMMMMMMMMMMMMMMMiiiiiiiiiiiMMMMMMMMMMMMMMMoMMMMMMMMMM
MMMMMiiiiiiiiiiiiiii

Batz's picture
User offline. Last seen 23 hours 49 min ago. Offline
Joined: 02/16/2012
Groups: Go Science
next time of course ;)

next time of course ;)

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