puzzle picture
359: Design the Pocket 1
Status: Closed


326jpower4 46 1373  13,0891
327xzhu19 46 1373  13,0891
328jlee392 46 1373  13,0891
329Pramunn1 46 1373  13,0891
330jsuh11 46 1373  13,0891
331nzaika1 46 1373  13,0891
332nflower3 46 1373  13,0891
333dmandel7 46 1373  13,0891
334xle1 46 1373  13,0891
335Jaxondug 46 1373  13,0891
336mlee161 46 1373  13,0891
337ldiazag1 46 1373  13,0891
338Sebastian2295 46 1373  13,0891
339Tpernes1 46 1373  13,0891
340mpark32 46 1373  13,0891
341wildcat445 46 1373  13,0891
342badileh1 46 1373  13,0891
343skwon17 46 1373  13,0891
344Koketa 46 1373  13,0891
345kreddy5 46 1373  13,0891
346shabibu1 46 1373  13,0891
347izhang2 46 1373  13,0891
348cyeung6 46 1373  13,0891
349dokola 46 1373  13,0891
350Nathaniel ... 46 1373 Montessori High School13,0891

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Joined: 08/29/2010
Is it intentional that the

Is it intentional that the ligand is locked in place?

I'm a new player, but in the previous design puzzle it was possible to wiggle or manually pull the ligand into an optimal location. Right now, it still seems to be possible to wiggle it around but at a drastically reduced rate (.001 per second about, for as long as you care to let it run).

The result is that I've done about 15 seconds of design, and a few hours of letting it wiggle as it is the only way to move things.

beta_helix's picture
User offline. Last seen 12 hours 17 min ago. Offline
Joined: 05/09/2008
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Everything is locked except for the designable sidechains

Unlike the previous design puzzles, we just want you to search for the sidechains that interact best with the ligand in this particular position.

I am sorry if that was unclear!

kbob's picture
User offline. Last seen 2 years 15 weeks ago. Offline
Joined: 09/03/2010
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What's the ligand?

What's the ligand?

Miedzix's picture
User offline. Last seen 7 years 14 weeks ago. Offline
Joined: 08/17/2010

ligand is that "thing" in the middle of protein
more here : http://en.wikipedia.org/wiki/Ligand :P

Joined: 09/07/2010
Groups: None

Any suggestions on what to do once Mutate side chains and Wiggle do not give any effect?

beta_helix's picture
User offline. Last seen 12 hours 17 min ago. Offline
Joined: 05/09/2008
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Mutate sidechains is the automated protocol, you must intervene

If you go into design mode and click on individual designable residues, you can mutate them manually.

This is where we need your help, because our computers can run "Mutate Sidechains" for hours and just get stuck. We are hoping that you can find interactions that "Mutate Sidechains" is unable to detect!

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