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549: Beginner Immunotherapy Design Puzzle 2
Status: Closed

Summary

Name: 549: Beginner Immunotherapy Design Puzzle 2
Status: Closed
Created: 04/26/2012
Points: 50
Expired: 05/04/2012 - 17:00
Difficulty: Beginner
Description: We are giving you a 8 residue long helix that you are able to mutate & dock onto the native binding region which is indicated by the side chains that are allowed to shake. Try to look for favorable hydrophobic interactions and strong hydrogen bonds, while maintaining the helix! If you are new to Foldit, make sure you have completed Intro Puzzle 5-2, and 7-1 through 7-4 before trying this puzzle. More info in the Puzzle Comments.
Categories: Design, Overall

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Comments

beta_helix's picture
User offline. Last seen 3 days 10 hours ago. Offline
Joined: 05/09/2008
Groups: None
More info:

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

Joined: 08/24/2011
Groups: Go Science
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.

EvdH's picture
User offline. Last seen 6 years 51 weeks ago. Offline
Joined: 03/30/2012
Groups: None
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.

Joined: 08/24/2011
Groups: Go Science
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.

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons