puzzle picture
359: Design the Pocket 1
Status: Closed


276elrohir 45 1438  13,0891
277Andrewer 45 1438  13,0891
278Pulse180 45 1438  13,0891
279FoldPrefect 45 1438 Contenders13,0891
280weurhartdezirez 45 1438  13,0891
281NinjaGreg 37 14 13,0891
282SOURAV 45 1438  13,0891
283budskijr 45 1438  13,0891
284cbwest 45 623  13,0891
285Handful 45 1438 Extraterrestrials13,0891
286DimitriM 45 1438 SETI.Germany13,0891
287LordSqueak 45 1438  13,0891
288dragon1988 45 1438  13,0891
289mechem 45 1438  13,0891
290Ryanfav 45 1438 Anthropic Dreams13,0891
291barzious 45 1438  13,0891
292tle27 45 1438  13,0891
293Steve2 45 1438  13,0891
294efuller8 45 1438  13,0891
295LeonardoDaVinci 45 1438  13,0891
296coconn10 45 1438  13,0891
297hmerchu1 45 1438  13,0891
298dangoe 45 1438  13,0891
299Placebo 45 1438  13,0891
300aakpat6 45 1438  13,0891

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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 11 hours 39 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 9 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 8 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
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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 11 hours 39 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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