puzzle picture
359: Design the Pocket 1
Status: Closed


101pppppppo_98 60 2065  13,46911
102SeTosha 60 2065  13,46811
1035ess 60 2065 xkcd13,46610
104Ujelet 60 2065  13,46510
105Ungoliant 60 2065  13,46410
106mmckenn9 60 2065  13,46210
107stormrobberee 60 2065  13,4619
108antlu65 60 2065  13,4619
109Perzik 60 2065 Boinc.be13,4609
110nblx 60 2065  13,4589
111Brick 60 2065 13,4558
112vlevran1 60 2065  13,4558
113grabhorn 60 2065  13,4558
114KuVaNi 60 2065  13,4528
115Georgas 60 2065  13,4528
116Chronosis 60 2065  13,4527
117cilamene 60 2065  13,4517
118Ozmandias 60 2065  13,4517
119alexob12 60 2065 Richard Dawkins Foundation13,4517
120Fluttershye 60 2065  13,4507
121SouperGenious 60 2065  13,4507
122NinjaGreg Clone 60 2065 13,4506
123Jim Fraser 60 2065 Contenders13,4506
124maxwell_thethird 60 2065 Richard Dawkins Foundation13,4506
125itskimo 60 2065 Anthropic Dreams13,4506

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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
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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
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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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