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870: 75 Residue Monomer Design: Strand-Locked
Status: Closed


Name: 870: 75 Residue Monomer Design: Strand-Locked
Status: Closed
Created: 04/03/2014
Points: 100
Expired: 04/10/2014 - 23:00
Difficulty: Intermediate
Description: This is a single-chain design puzzle with 75 residues, and four of the residues are locked into a beta-strand conformation. There are 2 filters enabled on this puzzle: the Residue IE Score monitors that all PHE, TYR, and TRP residues are scoring well, and the Core Existence filter checks that at least 25% of the residues are buried in the core of your design. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 3 designs that you want us to look at, even if they are not the best-scoring solutions!
Categories: Design, Overall

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gitwut's picture
User offline. Last seen 3 years 20 weeks ago. Offline
Joined: 05/18/2012
Groups: Contenders
Design issues

Granted, in the design stage perfectly straight strands are desirable but it's expected that they relax as the puzzle develops. Isn't there a way to lock the type of SS structure but keep its flexibility? Or is the inflexibility intentional?
If it is intentional, could you give us some insight as to why? Understanding why might help us to narrow our focus and come up with better solutions.

bkoep's picture
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Joined: 11/15/2012
Groups: Foldit Staff

You're correct, rarely do we see any final designs with perfectly ideal beta-strands. Solutions from this puzzle would need some refining before testing (perhaps in a follow-up puzzle?). Still, we wanted to mix it up a little in the design category, and this format presents a simple yet interesting challenge. We have some ideas for future puzzles that might be less restrictive.

Unfortunately, in the current client there is not a good way to put a "flexible lock" on one region of secondary structure. I agree, that would have been a more realistic challenge.

gitwut's picture
User offline. Last seen 3 years 20 weeks ago. Offline
Joined: 05/18/2012
Groups: Contenders

I like to use all types of SS for designing puzzles, but understand that scoring system favors helices. I'm not sure a follow-up would help unless there were some way to insure use of at least one strand.

It may be a silly question, as I don't understand the particulars of how bonuses or filters work, but can't there be a bonus or filter for having at least one strand of length "x" that would tip the helix bias?

spmm's picture
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Joined: 08/05/2010
Groups: Void Crushers
Rebuild Scripts choke on the sheet segs

Unless you can exclude the fixed segs the rebuliders choke, also idealising has to be done in a minimum of two sections. I am ok with having a sheet segment, just saying.

gitwut's picture
User offline. Last seen 3 years 20 weeks ago. Offline
Joined: 05/18/2012
Groups: Contenders

I'm guessing that by "choke" you mean they have no effect on the locked segments? None of the rebuild scripts I've used have abnormally ended. It's possible that the scripts I use exclude the locked segments, but I haven't checked.

In my original comment I had info about idealization issues, but removed it before posting. I extended the locked sheet by two segments in my design. I could click Idealize for each of the two additional segments, but couldn't use "Ideal SS" on them because it yields the message "Segment is locked". The result is a funky looking strand since the two segments bend, the locked ones don't and are perfectly straight.

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