puzzle picture
1378b: Hemagglutinin Binder Design: Loop Graft
Status: Closed

Summary

Name: 1378b: Hemagglutinin Binder Design: Loop Graft
Status: Closed
Created: 05/16/2017
Points: 100
Expired: 05/22/2017 - 23:00
Difficulty: Advanced
Description: Note: This puzzle replaces Puzzle 1378, which was incorrectly calibrated for scoring. Players may load in solutions from Puzzle 1378.

Design a protein that contains the provided hemagglutinin-binding loop! Hemagglutinin is a protein from the influenza virus. It is displayed on the surface of the virus capsid, and allows the virus to recognize and infiltrate human cells. One particular region of the hemagglutinin protein undergoes a dramatic shift during infection; it's thought that stabilizing this region (e.g. with a protein binder) can prevent the normal function of hemagglutinin and stop infection. In fact, during an influenza infection, the immune system can sometimes raise antibody proteins that bind this portion of hemagglutinin to defend against further infection. In this puzzle, we've provided a portion of the hemagglutinin protein, as well as a hemagglutinin-binding loop that is derived from one such antibody protein. We're asking Foldit players to design a new protein that incorporates this same loop!

The backbone and certain residues of the loop are fixed, and the loop is held in place with strong constraints. The starting structure of the design has 53 residues, but players may add residues up to a total of 63. Players may also delete and redistribute residues on either side of the prescribed binding loop. See the puzzle comments for filter details.
Categories: Design, Overall

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Comments

tokens's picture
User offline. Last seen 20 hours 14 min ago. Offline
Joined: 11/28/2011
Deleting residues

The puzzle comments say: "Players may also delete and redistribute residues on either side of the prescribed binding loop."

This is not possible for me. I could add residues, but not delete any residues, not even after I had added some.

bkoep's picture
User offline. Last seen 2 days 20 hours ago. Offline
Joined: 11/15/2012
Groups: None
Hmmm

That's unintended behavior. Can you delete specifically those residues that you added?

tokens's picture
User offline. Last seen 20 hours 14 min ago. Offline
Joined: 11/28/2011
Ahh, yes, I can delete the

Ahh, yes, I can delete the residues that I added, but not any other residues.

bertro's picture
User offline. Last seen 1 day 15 hours ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
Crash 1378b
LociOiling's picture
User offline. Last seen 59 min 39 sec ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
rebuild and remix seem to hang

Both rebuild and remix recipes seem to hang on the first rebuild or remix, never advancing. Cancel does not work, the message "cancelling" appears in the upper left, but it hangs there indefinitely.

This problem can be produced a manual remix. After selecting segments and starting remix, the first remix result is displayed, but remix hangs when you try to advance to the next result. Clicking the "X" to close remix has no effect. The only option is to close the client window, which seems to work normally.

In log.txt, a manual remix shows these results:

***** STARTING THREAD ActionBuild
lo,hi,size: 395,399,6
19 fragments found for fragment size 6
protocols.loops.loop_closure.ccd.RamaCheck: Initializing starting_rama_scores with current conformation.
SRVR_THRD getting notifications...
Sending SOPs:

Sending SOPs:

Couldn't quit: Illegal operation for this state (..\..\..\source\src\game\util\IRC.cc:375)
closing boinc...
Sending SOPs:

Sending SOPs:

exiting...
done.

The "illegal operation" message appears at the point where you manually close the client.

Attempting a manual rebuild crashed the client with the following in log.txt

***** STARTING THREAD ActionRebuild
protocols.loops.loop_closure.ccd.RamaCheck: Initializing starting_rama_scores with current conformation.

UNHANDLED EXCEPTION
  1: library_main +37712549 bytes (no line)
  2: library_main +28085694 bytes (no line)
  3: library_main +28085427 bytes (no line)
  4: library_main +28084834 bytes (no line)
  5: library_main +21461506 bytes (no line)
  6: library_main +21462889 bytes (no line)
  7: library_main +19008449 bytes (no line)
  8: library_main +17555767 bytes (no line)
  9: library_main +5749674 bytes (no line)
 10: library_main +5662462 bytes (no line)
 11: library_main +5664210 bytes (no line)
 12: library_main +5747910 bytes (no line)
 13: library_main +318776 bytes (no line)
 14: library_main +3253909 bytes (no line)
 15: library_main +3254363 bytes (no line)
 16: BaseThreadInitThunk +36 bytes (no line)
 17: RtlSubscribeWnfStateChangeNotification +1081 bytes (no line)
 18: RtlSubscribeWnfStateChangeNotification +1028 bytes (no line)

Running TvdL EDRW didn't cause a crash, but it did hang on the first rebuild.

actiasluna's picture
User offline. Last seen 15 hours 32 min ago. Offline
Joined: 03/05/2015
Groups: Gargleblasters
1378b crashes on remix or rebuild on Mac

Segmentation Fault 11... will post feedback. Crashed 3x... so this is still broken on my Mac

actiasluna's picture
User offline. Last seen 15 hours 32 min ago. Offline
Joined: 03/05/2015
Groups: Gargleblasters
Also observed the behavior Loci is describing above

when using some of the shake-wiggle-mutate functions... cancel or stop doesn't work (intermittent), ESC will stop or cancel.

kabubi's picture
User offline. Last seen 14 weeks 4 days ago. Offline
Joined: 11/29/2008
Groups: Void Crushers
can't see the player list too

can't see the player list too

Joined: 09/21/2011
Groups: Void Crushers
Sidechains of influenca part should be frozen (suggestion)

Shake takes forever, because it also shakes the big part.

gitwut's picture
User offline. Last seen 6 weeks 3 days ago. Offline
Joined: 05/18/2012
Groups: Contenders
Too slow, too buggy

I ran Local Quake on it for a while but the progress was way too slow (probably because of shake). I switched to Enhanced DRW on small subsets of the protein but encountered a crashes almost immediately. I don't currently have the inclination, patience or time to coddle this type of puzzle along.

mimi's picture
User offline. Last seen 9 hours 4 min ago. Offline
Joined: 11/17/2008
Groups: Contenders
Crash central

can't get it to stay up long enough to do much on it

Joined: 06/24/2008
Groups: Void Crushers
Crashes

I can not run and rebuild or reset scripts; I can not reset manually; I can rebuild manually though if I convert it to loop I can not manually rebuild. Also Idealize scripts seem to do nothing; though again I can manually Idealize.

On MAC.

Joined: 06/24/2008
Groups: Void Crushers
Oh yeh

I am devprev

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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, Microsoft, Adobe, RosettaCommons