Glycine making it hard to make good helices

Case number:845799-2012936
Topic:Biochem
Opened by:alcor29
Status:Open
Type:Suggestion
Opened on:Saturday, March 19, 2022 - 15:56
Last modified:Monday, March 28, 2022 - 21:33

Is anybody else experiencing this?

Since glycine is now loaded as allowed in sss, mutate programs are putting so many glycines in helices that they don't hold their shape and I'm having to spend too much time to try to get them to behave or to manually remove them one by one only to have a later mutate script put them back. Would appreciate knowing if it's just me.

(Sat, 03/19/2022 - 15:56  |  2 comments)


spvincent's picture
User offline. Last seen 6 hours 25 min ago. Offline
Joined: 12/07/2007
Groups: Contenders

I'm also seeing a lot of glycines appearing where they 'shouldn't'. In most cases I think it just means that things are packed too close.

Joined: 12/06/2008
Groups: Contenders

SPV is correct: you have your helices too close together when mutating.

To avoid this, don't mutate until after you've stabilized your poly-isoleucine structure. I never have glycines introduced when doing this, and I end up with a reasonable amount (10% or so) of alanines.

Sitemap

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