Why doesn't Blueprint tool make ideal loops between sheets?

Case number:845813-2011079
Topic:Game: Tools
Opened by:BootsMcGraw
Status:Open
Type:Question
Opened on:Monday, January 18, 2021 - 22:02
Last modified:Tuesday, January 19, 2021 - 05:59

I use the Blueprint tool to the exclusion of all others when I am first designing a protein. My latest (#1944) design has a 12-residue helix, plus five 5-residue sheets, plus another 12-residue helix. Each of the loops between these seven structures was also designed using the Blueprint tool.

I somehow have three un-ideal loops, all between the sheets. I have done nothing to the structure except to create it: no shake, no wiggle, no mutate. Nothing. Nada. Zip. Zilch. Why, then, if the Blueprint tool is supposed to provide us with ideal loops, do I have ANY un-ideal ones?

(Mon, 01/18/2021 - 22:02  |  5 comments)


jeff101's picture
User offline. Last seen 4 hours 9 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

The Feedback below is similar:

Building Blocks do not satisfy Ideal Loop filter
https://fold.it/portal/node/2003798

Joined: 12/06/2008
Groups: Contenders

Thanks for the quick response, Jeff. Should I close this feedback? The one you linked is almost four years old, and hasn't been addressed.

jeff101's picture
User offline. Last seen 4 hours 9 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

I'd leave it open. Having you bring it up again helps,
and having a link to an old but similar Feedback helps too.
The devs can close Feedbacks when they feel like they've
been addressed.

jeff101's picture
User offline. Last seen 4 hours 9 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

Below are some more articles about Ideal Loops:

How to make Ideal Loops
https://fold.it/portal/node/2002700

When is an ideal loop not an ideal loop?
https://fold.it/portal/node/2003031

When is an ideal loop not an ideal loop?
https://fold.it/portal/node/2003033

Odds are there are some wiki articles too.

Susume's picture
User offline. Last seen 6 days 1 hour ago. Offline
Joined: 10/02/2011

I learned only recently that the shape a blueprint block has when you drop it on the protein is not necessarily the shape that its constraint will pull to during a wiggle. I think the initial shape is to help backbone bonds form - once they are formed, and you wiggle, the constraint pulls things toward the actual 'ideal' shape, and I guess the score is supposed to help the bonds stay in place. So another question is, after adding the building block, mutating to good AAs for that loop, and giving it a shake and wiggle so the constraint can work, is it ideal then?

Those threads about ideal loops mostly pre-date the blueprint tool.

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, RosettaCommons