Mon, 09/13/2010 - 05:20
#2
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!
Mon, 09/13/2010 - 10:49
#3
What's the ligand?
What's the ligand?
Mon, 09/13/2010 - 15:30
#4
ligand
ligand is that "thing" in the middle of protein
more here : http://en.wikipedia.org/wiki/Ligand :P
Tue, 09/14/2010 - 00:27
#5
Any suggestions on what to do once Mutate side chains and Wiggle do not give any effect?
Tue, 09/14/2010 - 07:50
#6
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!
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.