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1903b: Two-sided Interface Design
Status: Closed


Name: 1903b: Two-sided Interface Design
Status: Closed
Created: 10/14/2020
Points: 100
Expired: 10/21/2020 - 23:00
Difficulty: Intermediate
Description: Note: This puzzle replaces Puzzle 1903, which had some errors in the puzzle setup. Players may not load solutions from Puzzle 1903.

Design an interface between two protein chains! This puzzle is a little different from our regular design puzzles. The starting structure includes two helical hairpins that are frozen in place and separated from one another. We want to build on these hairpins to create a binding interface between the two protein chains. However, the starting position of the hairpins is important, so the locked regions are held in place by strong constraints. The only way to make the two chains bind will be to fold up a brand new interface between them.

As you build on the two hairpins, it will be important to make a strong core with each chain, so that the chains fold up correctly. It will also be important to have a strong core at the interface where the two chains come together, so that they bind each other tightly. Keep an eye on the Core Existence Objective, which tracks all of these core residues together. Players may add up to 20 additional residues at a cost of 55 points per residue. See the puzzle comments for Objective details.
Categories: Design, Overall

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bkoep's picture
User offline. Last seen 19 hours 53 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff

Residue Count (max +1100)
Penalizes added residues at a cost of 55 pts per residue. Players may add up to 20 residues, for a total of 200.

Buried Unsats (max +500)
Penalizes polar atoms that cannot make hydrogen bonds, -150 points per atom (not including symmetric copies).

Core Existence: Total (max +5000)
Ensures that at least 25% of residues are buried in the core of the entire solution.

Interaction Energy (max +500)
Monitors that all large PHE, TYR, and TRP residues are scoring well.

SS Design (max +500)
Penalizes all CYS residues. Penalizes GLY, ALA residues in sheets. Penalizes GLY, SER, THR in helices.

Ideal Loops (max +500)
Penalizes any loop region that does not match one of the Building Blocks in the Blueprint tool. Use "Auto Structures" to see which regions of your protein count as loops.

infjamc's picture
User offline. Last seen 20 hours 37 min ago. Offline
Joined: 02/20/2009
Groups: Contenders
Seems that the penalty for

Seems that the penalty for buried unsats is actually 50 points each?

Joined: 09/29/2016
Groups: Gargleblasters


1903b addresses a problem with the puzzle (inherent to Foldit and its Pins), which causes Blueprints to move the Locked Helices bundle (Segments 1-90). Now the puzzle has Constraints, which are the many red lines you may see when using Blueprint Building Blocks.

Don't fret!
Here are two options to keep playing and not have your protein get flung around like a rag doll. PLEASE read through the post first, then decide which Solution will work best for you...

SOLUTION #1 (my personal choice
(1) Load puzzle 1903b / Reset the puzzle if you placed a Block already
(2) Open up the View Options menu
(3) Enable: 'Show backbone pins'
(4) Rotate the camera so you can see where the end of the first-chain's Loops (Segment 90),
(5) Click on the Pin at the end (it looks like a Backbone Issue bubble)

This will cause the Pin to jump to where it is supposed to be.
NOW you can go about playing the puzzle and using Blueprints.

NOTE: If you insert a Cut at at time in the first-chain, and use the Pins, make sure to click the pin again after closing your cuts, to ensure it returns back to it's proper place before you use any Blueprint Blocks again.

(1) Placed your Building Blocks to get the protein configured how you want it
(2) Press F to Freeze EVERYTHING
(3) Manually UnFreeze Segment 1 Sidechain AND Segment 90 Backbone and Sidechain
(4) Run Wiggle, and wait a moment for the Locked Helix bundle to settle back into its spot (may take 15-seconds or so)

The Freezing is so that your newly blueprinted stuff doesn't go zipping around when the Constraint bands (red lines) yank the Locked Helices back to where they're supposed to be.

Once it's settled back to its position, you're free to Unfreeze everything and go about your work.

Joined: 09/24/2012
Groups: Go Science
Thank you !!

Solution 2 works any time when trying to come back to the red constraints.
It works with clashing importance = 0

Joined: 12/06/2008
Groups: Contenders
non-ideal non-loop

The game is telling me that segments 90 and 91 are a non-ideal loop, and penalizing me 100 points. They are not even parts of the same structure!

Joined: 09/24/2012
Groups: Go Science
Don't loose time to try to idealize them

Even if I try making them all helices with ideal SS, they remain unideal loops.

Joined: 09/24/2012
Groups: Go Science

After clicking on them the pins go to the locked part and become locked ;(

Joined: 09/29/2016
Groups: Gargleblasters
Not a bug, per-se...

It's what I outlined in "Solution #1" where you click the pin to make it return to where it was INTENDED to be, it's on a locked segment, which in turn will nullify being able to move it. Because unlike, say, 1905 Aflatoxin, which has multiple Cuts to disjoint our workable chains from the locked protein, 1903/b lack those cuts, so we're bound by the same "1 Pin per Chain" rule :(

The "work around" for needing or wanting to use the pins in this instance, is to place a Cut in the workable protein right up against the Locked protein segment. Unfortunately, since we can't select the lock segment on one side, you'll have to use a Recipe to cut between the Locked residue and "Our" residue. :\

Doing that will temporarily give you access to another pin, that you can use however you're needing it. Just be sure to unlock it before you close, or its locked status could impact the Wiggle behavior. (I'm not 100% certain it will, in this instance, but I know that under certain circumstances, the place of a prior pin, after closing a cut, can still impact how the protein Wiggles.... REGARDLESS OF WHERE THE PIN'S LOCATION IS BEING DISPLAYED! Problem for us, in this instance, is that if we try to click the pin to Cycle through it's "previous locations", it's quite likely it will jump to the locked area.

However, the good news is that once it has jumped, that is now the pivot point, and it will again Wiggle as expected, since the game doesn't register the pin in a different spot from where it's rendering.
(Confusing, frustrating, and weird... I know)

Joined: 09/24/2012
Groups: Go Science
Infinite additional segments?

It seems that we are not limited by the number of added segments (on the cost of some bonus points). Cool !

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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