Please allow SOME alanines in designed helices.

Case number:671071-2010342
Topic:Game: Other
Opened by:BootsMcGraw
Status:Closed
Type:Suggestion
Opened on:Thursday, September 17, 2020 - 00:00
Last modified:Wednesday, April 13, 2022 - 17:07

We discussed in some of the puzzle comments that having alanine-rich helices may form a good, tight core, but they are not so good in other ways.

There are times when I am working a design puzzle where an alanine seems to be exactly what I need for what I'm trying to attempt. Do I really need to take a fifty point penalty for adding an alanine to my design, when it is the most common amino acid in helices?

I propose keeping a penalty function for alanines in a helix, but only if the helices contain over a certain percentage (5%? 10%) of alanines. Who's with me on this? Hit the up arrow button, below.

(Thu, 09/17/2020 - 00:00  |  3 comments)


Joined: 12/06/2008
Groups: Contenders
Status: Open » Closed

This has been implemented in early 2022, with no restrictions on the number of alanines (also glycines... but who wants those?) in helices and sheets. Thank you.

A caveat to players: Now that you can stick alanines into design puzzles, make sure your secondary structures are not too closely packed, or the mutate function will replace too many of the residues with alanine or glycine.

Keeping this feedback open for a week or two longer to give players a chance to review it.

Joined: 12/06/2008
Groups: Contenders
Status: Closed » Open

Re-opening, for a short time.

Joined: 12/06/2008
Groups: Contenders
Status: Open » Closed

Now closing. If you didn't get to read this... sorry... your loss. You snooze, you lose!

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