puzzle picture
359: Design the Pocket 1
Status: Closed


151tedeum 60 2063  13,4383
152Heaton 60 2063  13,4383
153leck 60 2063  13,4383
154Doragan 60 2063  13,4383
155weitzen 60 2063  13,4383
156rworthi 60 2063  13,4383
157Bolo1910 60 2063  13,4372
158nchartier 60 2063 L'Alliance Francophone13,4372
159eunchul 60 2063  13,4372
160james1galvin 60 2063  13,4372
161porcopazzo 60 2063  13,4372
162NIK1987 60 2063  13,4362
163xbq 60 2063  13,4362
164Tamison 60 2063 Anthropic Dreams13,4362
165CoachB 60 2063  13,4362
166Lumir 60 2063 Czech National Team13,4362
167jhullaert 60 2063  13,4362
168Fienesse 60 2063  13,4352
169splav 60 2063  13,4352
17024grant24 60 2063  13,4352
171yuda 60 2063  13,4352
172grastgirl 60 2063  13,4352
173tjohnson 60 2063 Mmm Helix Fries.13,4342
174martinf 60 2063  13,4342
175Ucuri 60 2063  13,4342

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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 3 hours 10 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 1 year 45 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 6 years 44 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 3 hours 10 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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