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Recipe: Design Models 2.3.1
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Name: Design Models 2.3.1
ID: 101066
Created on: Tue, 06/02/2015 - 16:21
Updated on: Thu, 08/06/2020 - 09:31

Proposes a secundary structure for current length

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Joined: 09/24/2012
Groups: Go Science

The proposed SS is based on following basic preferences:

-1 loop at each end
-3 loops between sheets (SS)
-4 loops between helixes (HH), and between helix and sheet (HS)
-helix length = 2 * sheet length

Joined: 09/24/2012
Groups: Go Science
Corrected following blueprint

-1 loop each end
-2-4-5 loops between sheets
-1-2-3 loops between helices
-2-3 loops between sheets and helices

Joined: 09/24/2012
Groups: Go Science

The recipe only proposes designs where there is a reasonable amount of sheets for each helix (minimum 2 sheets per helix) and a reasonable core potential. Only exact matching of above preferences are proposed, unless for very common structure (e.g. SSHSS), where a solution with extra loops could be proposed (up to 5 loops around an helix).

The current version only proposes the following:
- 50 and 70 residues: (SHS and SSHSS)
I will update it when needed for new puzzles.

The SS is archived in note 19. It can be recovered at any time using Reset my SS in note 19 _GS.

Joined: 09/24/2012
Groups: Go Science
User guide for further design

1) On a reset of the puzzle, run the recipe and select to design you like (e.g. SHS, 2 sheets and one crossing helix)

Now it's time to hand fold (did you expect to escape hand fold ?!?)

2) tool "Ideal SS" on each helix

3) You might freeze all helices and sheets if you want to use bands

4) Cut in the loops - or use bands - in order to align the sheets and make H-bonds

5) Align the helices along the sheets

6) Quickfix

Joined: 09/24/2012
Groups: Go Science

More models for 70 residues. Now:
(not always a loop at each ends)

Joined: 09/24/2012
Groups: Go Science

Models for 50, 55, 60, 65, 70, 75 and 80 segments puzzles.
Added HHH models for all of them (can be interesting for symmetric H-Bond puzzles)

Joined: 09/24/2012
Groups: Go Science

all HHSSSS now available

Joined: 09/24/2012
Groups: Go Science

bug fixed

Joined: 09/24/2012
Groups: Go Science

Added lengths 85 & 90 residues

Joined: 09/24/2012
Groups: Go Science

fixed HHSSS in 80-85-90 sorry

Joined: 09/24/2012
Groups: Go Science

added HHSSSSH in 80-85-90

Joined: 09/24/2012
Groups: Go Science

ver 1.0.11 corrected the length of sheets in order to respect chirality in 85 + test bands
ver 1.1.0 Adding different paterns for choice of direction and chirality, e.g. HHSSS, SSSHH, HSSSH
Note: in SSS, when the number of residues is pair (for a connecting loop of 3 segments) , we can do a good
cake turning left, then right then left ...
If it is uneven, it does not work (has to turn always left or always right).
That's what I tried to correct in this verion
Moreover, I've seen in top solutions that HSSSH can be as good as SSSHH or HHSSS
As chirality has its importance, I made several similar structures but in opposite directions as well.
The default loops are : 3 segments for connecting sheets, 4 segments for connecting Helices (to sheet or helice) and
one segment at each end. From this basic designes, it's possible to idealize chang turns by transforming loop segments to sheets.
The rules are: SS link: 2-3 => turn left (from residue n to n+1 with sidechains pointing bellow)
4 segs= 50-50
5 segs: turning right (=> replacing the 2 sheet ends with loops doesn't solve chirality problem)
HS link (2-3-4 loop length): the sidechain of the forst sheet seg must point away from helix
(use this rule to decide on which side of the plane you put your helix)
SH link (2 loop length): the helix is where the latest S seg's sidechain points to
SH link (3 loop length): the helix goes opposite of the last sheet sidechain.

Joined: 09/24/2012
Groups: Go Science
ver 2

SS compatible with blueprint: 2-4-5 segs only for SS(never 3), 1-2-3 only for HH

And still compatible with the chirality problem and about 2 helix residues for one sheet residue.

Joined: 09/24/2012
Groups: Go Science
ver 2.2

Corrected some SSs

Joined: 09/24/2012
Groups: Go Science

added soms SS.
Tip: start with a length of a multiple of 5 (and add 5 segments to the given structure), run the recipe and choose your SS.
Ideal SS all sheets and helices.
Then use Blueprint tool for sheets.
If the loop length between helices is too short (1 or 2 would be too short for core filter), or if the link between sheets and helices (or between sheets) is not nice, add a segment in the loop and try Blueprint again.

Freeze the nice structures and loops. Add bands between sheets. Clashing importance to 0.1, wiggle backbones until most sheet loops are ideal (check the filter ideal loop to see on screen).

Use remix to try to fix unideal loops. If it does not work, add or delete residues in the loop and try again. If it doesn't work, Autostructure and try again.

CI 1, mutate all. Wiggle all.Mutate all. Shake all.

If there remain unideal loops, delete of add segments, remix, autostrucure, try again or run Find Starting Filter recipe if you have no time.

Joined: 09/24/2012
Groups: Go Science

Adapted for binder designs (only set SS for unlocked segments if unlocked are on last segments)

Joined: 06/06/2013
Groups: Gargleblasters
thanks for sharing

Thanks Bruno :) This is much better than our old starter recipes which didn't address ideal loops at all

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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, RosettaCommons