puzzle picture
359: Design the Pocket 1
Status: Closed


176Fred Erik 62 2044  13,4342
177pperin 62 2044  13,4341
178hazarius 62 2044 Ukraine13,4331
179Januar2 62 2044  13,4331
180Nachtrot 62 2044  13,4321
181agl 62 2044  13,4321
182Ladenhorcher 62 2044 Crunching Family13,4321
183meddy2065 62 2044  13,4321
184Erako 62 2044  13,4321
185Histone17 62 2044  13,4321
186n0cand3fend 62 2044  13,4311
187deus911 62 103 Richard Dawkins Foundation13,4311
188Das13messer 62 2044  13,4301
189CureET 62 2044  13,4301
190BuzzDee 62 2044 SETI.Germany13,4301
191gangsterfabrik 62 2044  13,4291
192Nordic_Alf 62 2044 SETI.Germany13,4281
193attackgorilla 62 2044  13,4281
194xgirl 62 2044  13,4281
195Thorayon 62 2044  13,4281
196kwb02565 62 2044  13,4281
197vsviridov 62 2044  13,4271
198BlinkyWatts 62 2044  13,4271
199exer 62 2044 Russian team13,4271
200mmalaba1 62 2044  13,4271

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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 20 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 44 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 43 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 2 hours 20 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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