puzzle picture
359: Design the Pocket 1
Status: Closed


201techmaster 62 2091  13,4271
202evolutionofaudrey 62 2091  13,4261
203liamo14 62 2091  13,4261
204JeNNeR 62 2091  13,4261
205tim1079 62 2091  13,4261
206purplearcanist 62 2091  13,4261
207snovvfall 62 2091  13,4261
208SubaruKid 62 2091  13,4251
209Toures 62 2091  13,4251
210smaragdkek 62 2091  13,4241
211crispy fry 62 2091  13,4241
212TheedMan 62 2091  13,4241
213sacredcow 62 2091  13,4241
214simonstpauli 62 2091  13,4241
215identy 62 2091  13,4241
216Danielnator 62 2091  13,4241
217Gray Thomas 62 2091  13,4241
218thosi 62 2091  13,4231
219auton1 62 2091  13,4231
220mariuszsam 62 2091  13,4231
221Ahura Mazda 62 2091  13,4231
222The Red&nb... 62 2091  13,4211
223JPP 62 2091 L'Alliance Francophone13,4211
224Teophparask 62 2091  13,4211
225zonk77 62 2091  13,4201

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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 1 day 18 hours 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
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 1 day 18 hours 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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