puzzle picture
359: Design the Pocket 1
Status: Closed


226ersophot 45 1449  13,4201
227jonhunse 45 1449  13,4201
228someguy57 45 1449  13,4201
229currius 45 1449  13,4191
230vbhaske1 45 1449  13,4171
231cbrady11 45 1449  13,4111
232rwillett 45 1449 Richard Dawkins Foundation13,3911
233Lascari 45 1449  13,3701
234Revent 45 1449  13,3491
235mgrahamg 45 1449 Super Happy Fun Time13,3421
236jkoh5 45 1449  13,3071
237h_elkhadem 45 1449  13,2961
238Entropic Decay 45 1449  13,2691
239msong8 45 1449  13,2491
240SpaceOddity 45 1449  13,2481
241Datamine 45 1449  13,2251
242haobian 45 1449  13,2001
243jetten1 45 1449  13,1871
244kurtdebruyne 45 1449  13,1741
245nbuzinsky 45 1449  13,1591
246armadillo314 45 1449  13,1581
247yafkari1 45 1449  13,1561
248poiuytrewq 45 1449  13,1401
249dmille96 45 1449  13,1371
250bobbido 45 1449  13,1371

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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 2 hours 8 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
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 2 hours 8 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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