549: Beginner Immunotherapy Design Puzzle 2

Since the first Immunotherapy Design Puzzle (539) gave really interesting results, we start off with a new one in this series. The goal is again to find a solution which binds the CTLA-4 protein (more background here: http://fold.it/portal/node/992285), however you are now targeting the native binding site of the CTLA-4 protein. Nature already came up with a beta-sheet which is capable of binding this region, we are now searching for a helix to interact with the site.

and please check out the blogpost about this: http://fold.it/portal/node/992498

Tue, 05/01/2012 - 15:31

#152

mbinfield 126 2204

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Binding site

In a future iteration, can we have slightly weaker constraints on the binding site? I'd like to work in the area around 91, which is just far enough away that the constraint makes it difficult, but I think you could get good interactions there.

Tue, 05/01/2012 - 23:26

#153

EvdH 136 7430

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It is indeed an interesting

It is indeed an interesting area with the hydrophobic over there, but since Ile91 is relatively far away from the natural binding site, it is constrained in this puzzle.

Fri, 05/04/2012 - 23:50

#154

mbinfield 126 2204

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Thanks

Ah, thanks. I was thinking maybe it would still be close enough to interfere with the natural binding site, maybe depending on the backbone behind the helix.