puzzle picture
1499c: Symmetric Dimer Design: Hydrogen Bond Networks
Status: Closed

Summary

Name: 1499c: Symmetric Dimer Design: Hydrogen Bond Networks
Status: Closed
Created: 03/21/2018
Points: 100
Expired: 03/27/2018 - 23:00
Difficulty: Intermediate
Description: Note: This puzzle replaces Puzzle 1499 which was posted with a problematic filter. Players may load in solutions from Puzzle 1499.

This symmetric design puzzle has C2 symmetry, with two symmetric chains. The H-bond Network Filter encourages players to bury satisfied H-bond networks at the interface between the two chains. There are several other filters in effect; see the puzzle comments for details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!
Categories: Design, Overall, Symmetry

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Comments

bkoep's picture
User offline. Last seen 10 hours 53 min ago. Offline
Joined: 11/15/2012
Groups: None
Filters

Core Existence: Monomer: Ensures that at least 27% residues are buried in the core of the monomer unit.

Core Existence: Complex: Ensures that at least 31% residues are buried in the core of the entire complex (including the interface between monomer units).

HBond Network: Rewards networks comprising at least three hydrogen bonds. Up to four hydrogen bonds may span the interface between chains. Networks must at least 50% satisfied (i.e. 50% of all polar atoms in a network must make a hydrogen bond).

jeff101's picture
User offline. Last seen 16 hours 5 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
What are the possible scores for each Filter?

What are the possible scores for each Filter?
Do the Core Existence Filters each have 2 values:
one if satisfied & another if not satisfied?
Does the HBond Network Filter also have 2 values:
one if satisfied & another if not satisfied?
What are the lowest and highest possible Filter
Score Totals one can get on 1499c?

Thanks!

Joined: 06/24/2008
Groups: Void Crushers
Still weird

1499c is still acting weird. I shared it with scientist so you can look.

bkoep's picture
User offline. Last seen 10 hours 53 min ago. Offline
Joined: 11/15/2012
Groups: None
Thanks!

Is this the same bug you mentioned in the original puzzle 1499?
http://fold.it/portal/node/2004908#comment-36421

Do you have any cutpoints in your structure? Some players have discovered that, when cutpoints are in place, certain parts of the active chain are unable to move (although, apparently, parts of the symmetric chain can still be moved).

Joined: 06/24/2008
Groups: Void Crushers
cut points

yes i was trying to move a part around. i shared the puzzle with scientists

jeff101's picture
User offline. Last seen 16 hours 5 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Finding the monomers:

In this puzzle and 1499, when the monomers are far apart, it has sometimes been hard to find the main monomer. It would help if there were lines (sort of like disabled bands) connecting the main monomer to each of its copies. It would also help if one could make bands from the copies to the main monomer. Right now, it seems like I can only make bands from the main monomer to its copies, but sometimes I find the copy before I find the main monomer.

It helps to add labels to each monomer. You can even have the notes for AA#1 on the copied monomer be different from the notes for AA#1 on the original monomer. These labels can be displayed in Note Mode to help find the monomers when they go off the screen.

In the original interface, if you tab on a residue, it shows notes for that residue. You can also use the arrows to scan through the notes for all the other residues. On the main monomer, the scanning stops when it reaches the ends. On the copied monomer, if you overshoot the ends, the notes disappear, and you have to re-tab on a residue to see the notes again. It would help if the arrows behaved on the monomer copies the same as they behave on the main monomer. It might help more if you could use the arrows to scan through one monomer's notes and then, if you go past the end residues on that monomer, it starts showing the notes for the copied monomers. It could be cyclic so if you start with the Notes on AA#1 of the main monomer and keep pressing the right arrow, you would see the main monomer's Notes for AA#1 to the end, then copy 1's Notes for AA#1 to the end, then copy 2's Notes for AA#1 to the end, etc., and eventually you would see the main monomer's Notes again.

I think it would also help to have the Home key always center the main monomer on the screen. Right now, it centers some other point on the screen, and this is not usually helpful when the monomers are far apart.

Thanks!

jeff101's picture
User offline. Last seen 16 hours 5 min ago. Offline
Joined: 04/20/2012
Groups: Go Science
Let LUA make bands between monomers:

It would also help if we could use LUA commands to make bands between atoms on the original monomer and atoms on a copied monomer.

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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, Microsoft, Adobe, RosettaCommons