Joined: 06/17/2010
And comments

are where?
We have to bind it or lock it inside? Or both?

beta_helix's picture
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Joined: 05/09/2008
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sorry for the delay on this!

The main comment is not to worry about the clash between Residue 219 and the ligand (Residue 258) as well as the other clash between 216 and 237. Those are fixed and everyone will have them so there is no need to try and get rid of them.

As you can see, the bottom of the ligand (where the clash is) has very strong constraints to stay in that position, but we actually have no idea where the other end of the ligand is (the section that interacts with the loop you are designing), so you are free to move that end (without disturbing the part of the ligand that bonds to Lysine 219).

Anything you can do with the loop to improve the interaction energy with the ligand would be very useful!

Joined: 08/24/2011
Groups: Go Science
If I move the outer end of

If I move the outer end of the ligand more than a tiny amount, it still moves the inner end enough to break whatever fix you coded to ignore the clash at 219, and the score drops into massive negative. That makes it hard to position the ligand at all.

Joined: 11/20/2011
Groups: None
cool

The main comment is not to worry about the clash between Residue 219 and the ligand (Residue 258) as well as the other clash between 216 and 237. Those are fixed and everyone will have them so there is no need to try and get rid of them.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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