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884: 74 Residue Ebola Binder Design
Status: Closed

Summary

Name: 884: 74 Residue Ebola Binder Design
Status: Closed
Created: 05/01/2014
Points: 0
Expired: 05/08/2014 - 23:00
Difficulty: Intermediate
Description: This is a design puzzle similar to Puzzle 879—now with 74 residues—near the interface of a target glycoprotein from the Ebola virus. At the binding site of the Ebola protein, there is already a helix designed by scientists in the Baker Lab, but the helix will not fold up by itself! Build a scaffold around the starting design that will fold up properly and stabilize the binding helix! There are strong constraints to keep the binding helix in place, and you may not mutate residues at the interface. You may not add additional residues to the design, but you may delete residues from one end of the design and reinsert them at the other end. This puzzle includes a Residue IE Score filter and a Core Existence filter, and High Wiggle Power has been disabled. Remember to share your favorite designs using the Share with Scientist tool, even if those are not your best-scoring solutions!
Categories: Design, Overall

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Comments

wisky's picture
User offline. Last seen 1 year 4 weeks ago. Offline
Joined: 07/13/2011
Core exists filter

Core exists filter appears to be taking into account residues from the ebola protein. The highest I was able to get it to with my current design was -480.

Joined: 10/30/2012
Groups: Beta Folders
is it just me or is this kind

is it just me or is this kind of slow and stiff

spmm's picture
User offline. Last seen 4 weeks 5 days ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
2 dumb questions

The 104 - 106 segments - do we need to keep away from them because there is actually something there?

Seg 1 - serine - is that going to be connected to something else so needs room to do that?
thanks

Joined: 09/21/2011
Groups: Void Crushers
Score issues

1. The ebola part of the score is so negative that normal scoring and seeing how far pointswise you are on the scoring ladder is not possible as long as the total score is negative.
This should be corrected.
2. The filters should only work on the design part of the puzzle, not on the Ebola part. (would probably also speed up the puzzle).
3. As a consequence of 1 scripts that cant cope with negative scores or change behavior depending on the score don't work correctly.
(TIP for my DRW users: use More options and disable skip fuze and replace qstab)

bkoep's picture
User offline. Last seen 2 days 23 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Puzzle closed

This puzzle has been closed and reposted with relaxed requirements for the Core Exists filter and raised baseline score:

http://fold.it/portal/node/997612

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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, Boehringer Ingelheim, RosettaCommons