puzzle picture
359: Design the Pocket 1
Status: Closed


251triciabuk 45 1438  13,1181
252djtimm 45 1438  13,1081
253Cake or&nb... 45 1438  13,1031
254ruud 45 1438  13,1031
255Misiek96 45 1438  13,0991
256jjiao1 45 1438  13,0991
257spy club 45 1438 13,0991
258goobea 45 1438  13,0931
259ceventer 45 1438  13,0891
260aspadistra 45 544 DSN @ Home13,0891
261digitalmad 45 1438 Richard Dawkins Foundation13,0891
262redrover 45 1438  13,0891
263was_fired 45 1438  13,0891
264test_account1 45 544 test_group113,0891
265kingfisher9704 45 1438 Void Crushers13,0891
266mr.bean 45 1438  13,0891
267heyubob 45 351  13,0891
268NR22 45 1438  13,0891
269Dantes 45 1438  13,0891
270protagoras70 45 1438  13,0891
271clil16 45 1438  13,0891
272cfried11 45 1438  13,0891
273ilya.makedon 45 1438  13,0891
274Mudface 45 1438  13,0891
275rikrdo89 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 3 hours 52 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 3 hours 52 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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